From e3bfb285853a2d6ad7fd87c236bf553334cf720a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 15:50:44 +0100 Subject: [PATCH 1/8] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 52950a95..daa49a4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,6 +42,7 @@ Initial release of nf-core/references, created with the [nf-core](https://nf-co. - [48](https://github.com/nf-core/references/pull/48) - Simplify VCF tabix index generation and related assets - [48](https://github.com/nf-core/references/pull/48) - Code refactoring (new subworfklows for each type of operations) - [49](https://github.com/nf-core/references/pull/49) - Better publishing for all files +- [53](https://github.com/nf-core/references/pull/53) - Better publishing for all aligner indexes ### Fixed From 61150cf4e56df85e7d8b699e77367bdf24660cdf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 15:51:18 +0100 Subject: [PATCH 2/8] Better publishing for all aligner indexes --- main.nf | 20 +++---- tests/hisat2.nf.test.snap | 38 ++++++------- tests/kallisto.nf.test.snap | 8 ++- tests/multiple.nf.test.snap | 24 +++++---- tests/rnaseq.nf.test.snap | 62 +++++++++++---------- tests/rsem.nf.test.snap | 104 +++++++++++++++++++----------------- tests/salmon.nf.test.snap | 76 +++++++++++++++----------- tests/sarek.nf.test.snap | 44 ++++++++------- 8 files changed, 205 insertions(+), 171 deletions(-) diff --git a/main.nf b/main.nf index fd71eb93..d5eddd40 100644 --- a/main.nf +++ b/main.nf @@ -103,19 +103,19 @@ workflow { output { 'bowtie1_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BowtieIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BowtieIndex/version1.3.1" } } } 'bowtie2_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Bowtie2Index/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Bowtie2Index/version2.5.2" } } } 'bwamem1_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BWAIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BWAIndex/version0.7.18" } } } 'bwamem2_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BWAmem2Index/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BWAmem2Index/version2.2.1" } } } 'dragmap_hashmap' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/dragmap/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/dragmap/version1.2.1" } } } 'fasta' { path { meta, fasta -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/WholeGenomeFasta/${file}" } } @@ -133,13 +133,13 @@ output { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } } } 'hisat2_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/version2.2.1" } } } 'intervals_bed' { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/intervals/${file}" } } } 'kallisto_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1" } } } 'msisensorpro_list' { path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/msisensorpro/${file}" } } @@ -154,16 +154,16 @@ output { path { folder -> { file -> "multiqc/multiqc_report" } } } 'rsem_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/version1.3.1" } } } 'salmon_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/version1.10.3" } } } 'splice_sites' { path { meta, txt -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SpliceSites/${file}" } } } 'star_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/version2.7.11b" } } } 'transcript_fasta' { path { meta, fasta -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/TranscriptFasta/${file}" } } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 5b9d221f..6f641664 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -17,14 +17,15 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -52,7 +53,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T12:55:26.231501216" + "timestamp": "2024-12-05T15:35:30.36657085" }, "Run with profile test for hisat2 | --input GRCh38_chr21.yml": { "content": [ @@ -81,14 +82,15 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites/GRCh38_chr21.splice_sites.txt", "multiqc", @@ -120,6 +122,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T13:57:17.25040689" + "timestamp": "2024-12-05T15:36:59.914837757" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 6d9f860d..20e1bb87 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -27,6 +27,7 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -42,6 +43,7 @@ ], [ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", + "version0.51.1:md5,4adc522fa0fdaace79e45bcee7abb865", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] @@ -50,7 +52,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:31:39.422746281" + "timestamp": "2024-12-05T15:37:47.995242455" }, "Run with profile test for kallisto | --input assets/test/default_extended.yml": { "content": [ @@ -70,6 +72,7 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -82,6 +85,7 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "version0.51.1:md5,e425f39ad34d95970acdb16a706dfbb9", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], @@ -89,6 +93,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:31:07.501838885" + "timestamp": "2024-12-05T15:37:21.239733377" } } \ No newline at end of file diff --git a/tests/multiple.nf.test.snap b/tests/multiple.nf.test.snap index aa113a17..f955c6cf 100644 --- a/tests/multiple.nf.test.snap +++ b/tests/multiple.nf.test.snap @@ -78,11 +78,12 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/intervals/GRCh38_chr21.bed", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/GRCh38_chr21.amb", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/GRCh38_chr21.ann", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/GRCh38_chr21.bwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/GRCh38_chr21.pac", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/GRCh38_chr21.sa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18/GRCh38_chr21.amb", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18/GRCh38_chr21.ann", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18/GRCh38_chr21.bwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18/GRCh38_chr21.pac", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BWAIndex/version0.7.18/GRCh38_chr21.sa", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.dict", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.fai", @@ -92,11 +93,12 @@ "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Annotation/intervals/testdata.GRCh38_chr22.bed", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.amb", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.ann", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.bwt", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.pac", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.sa", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.amb", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.ann", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.bwt", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.pac", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.sa", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.dict", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta.fai", @@ -135,6 +137,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-02T12:27:31.034085088" + "timestamp": "2024-12-05T15:38:53.100305759" } } \ No newline at end of file diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index c9a4f075..9bd41e0d 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -34,36 +34,39 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.1.bt2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.2.bt2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.3.bt2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.4.bt2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.rev.1.bt2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/GRCh38_chr21.rev.2.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.1.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.2.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.3.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.4.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.rev.1.bt2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Bowtie2Index/version2.5.2/GRCh38_chr21.rev.2.bt2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.1.ebwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.2.ebwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.3.ebwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.4.ebwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.rev.1.ebwt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/GRCh38_chr21.rev.2.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.1.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.2.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.3.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.4.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.1.ebwt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.2.ebwt", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.fai", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.sizes", @@ -93,6 +96,7 @@ "GRCh38_chr21.rev.1.ebwt:md5,5e5a45602d63d358e3edca7cdb683a1b", "GRCh38_chr21.rev.2.ebwt:md5,1e5088944137b3277e65306ea1a347a5", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", + "Log.out:md5,906d176b72e2bacef56c036a8c278644", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,1c9cd646313f1abb1cfc205ccab73464", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -116,6 +120,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:36:21.378903247" + "timestamp": "2024-12-05T15:41:12.239111965" } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 74400b51..3a417e8e 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -18,30 +18,31 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -56,6 +57,7 @@ [ "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", + "Log.out:md5,63ebdd9d823e1bc2929aa0ba93c995e1", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -84,7 +86,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:38:25.050066105" + "timestamp": "2024-12-05T15:42:50.995387106" }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ @@ -115,30 +117,31 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -156,6 +159,7 @@ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", + "Log.out:md5,810ffedc0e26770f9b71923e55f55152", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -185,6 +189,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:41:05.19761261" + "timestamp": "2024-12-05T15:44:39.234286812" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 39255a22..851fbc18 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -27,21 +27,22 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -58,14 +59,19 @@ [ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", + "ctable.bin:md5,365045f97860044295656c7cc8babf81", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", + "pos.bin:md5,388eac191e3fdf5c22b6b4c222e83de0", + "pre_indexing.log:md5,a44f369e65821a957131940c7741055c", "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", + "ref_indexing.log:md5,ee5a550ddededd200b63a2376bc59ca9", "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", + "seq.bin:md5,5d9e283968d9bcd0a766cff289d61d2f", "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" @@ -75,7 +81,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:43:57.125501449" + "timestamp": "2024-12-05T15:46:46.179472015" }, "Run with profile test for salmon | --input assets/test/default_extended.yml": { "content": [ @@ -95,21 +101,22 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -123,14 +130,19 @@ ], [ "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", + "ctable.bin:md5,a5f381189da767e61e32a187459a5cce", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", + "pos.bin:md5,ac2d0c717b65b7e93e7f1b289a4303c5", + "pre_indexing.log:md5,8011b3770d6ca53e60fbbe9fcbb0266d", "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", + "ref_indexing.log:md5,be29c64b496ce13846959ba4c0c1678d", "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", + "seq.bin:md5,c335689351bd0a27c3220ea1c5eafc65", "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] @@ -139,6 +151,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T14:42:43.661220781" + "timestamp": "2024-12-05T15:45:46.523172582" } } \ No newline at end of file diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap index 1876a837..fcc5c8a0 100644 --- a/tests/sarek.nf.test.snap +++ b/tests/sarek.nf.test.snap @@ -47,29 +47,32 @@ "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Annotation/msisensorpro/testdata.GRCh38_chr22.msisensor_scan.list", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.amb", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.ann", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.bwt", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.pac", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/genome.sa", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.amb", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.ann", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.bwt", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.pac", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAIndex/version0.7.18/genome.sa", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/genome.fasta.0123", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/genome.fasta.amb", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/genome.fasta.ann", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/genome.fasta.bwt.2bit.64", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/genome.fasta.pac", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1/genome.fasta.0123", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1/genome.fasta.amb", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1/genome.fasta.ann", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1/genome.fasta.bwt.2bit.64", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/BWAmem2Index/version2.2.1/genome.fasta.pac", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.dict", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/WholeGenomeFasta/genome.fasta.fai", "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/hash_table.cfg", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/hash_table.cfg.bin", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/hash_table.cmp", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/hash_table_stats.txt", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/ref_index.bin", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/reference.bin", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/repeat_mask.bin", - "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/str_table.bin", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/hash_table.cfg", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/hash_table.cfg.bin", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/hash_table.cmp", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/hash_table_stats.txt", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/ref_index.bin", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/reference.bin", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/repeat_mask.bin", + "Homo_sapiens/nf-core/references/testdata.GRCh38_chr22/Sequence/dragmap/version1.2.1/str_table.bin", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -99,7 +102,10 @@ "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070", "genome.dict:md5,2433fe2ba31257337bf4c4bd4cb8da15", "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685", + "hash_table.cfg:md5,9b55cf0e9be8b4afbcb80dcd1189293a", + "hash_table.cfg.bin:md5,111788e4f8f8e1745966a4f7d837e23b", "hash_table.cmp:md5,1caab4ffc89f81ace615a2e813295cf4", + "hash_table_stats.txt:md5,fd8b502fdd0fa8070cbf207dec8597af", "ref_index.bin:md5,dbb5c7d26b974e0ac338024fe4535044", "reference.bin:md5,be67b80ee48aa96b383fd72f1ccfefea", "repeat_mask.bin:md5,294939f1f80aa7f4a70b9b537e4c0f21", @@ -111,6 +117,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-02T11:21:36.124482055" + "timestamp": "2024-12-05T15:48:02.521229914" } } \ No newline at end of file From a105b537c18fbfd4c9ba352642b91585ca2f64c8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 15:56:31 +0100 Subject: [PATCH 3/8] fix kallisto --- main.nf | 2 +- tests/.nftignore | 22 +++++++++++----------- tests/kallisto.nf.test.snap | 8 ++++---- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/main.nf b/main.nf index d5eddd40..632fc667 100644 --- a/main.nf +++ b/main.nf @@ -139,7 +139,7 @@ output { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/intervals/${file}" } } } 'kallisto_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1/${file}" } } } 'msisensorpro_list' { path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/msisensorpro/${file}" } } diff --git a/tests/.nftignore b/tests/.nftignore index a9cf3352..94dd6057 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,14 +1,14 @@ -**/KallistoIndex -**/RSEMIndex/Log.out -**/STARIndex/Log.out -**/SalmonIndex/ctable.bin -**/SalmonIndex/pos.bin -**/SalmonIndex/pre_indexing.log -**/SalmonIndex/ref_indexing.log -**/SalmonIndex/seq.bin -**/dragmap/hash_table.cfg -**/dragmap/hash_table.cfg.bin -**/dragmap/hash_table_stats.txt +**/kallisto +**/RSEMIndex/*/Log.out +**/STARIndex/*/Log.out +**/SalmonIndex/*/ctable.bin +**/SalmonIndex/*/pos.bin +**/SalmonIndex/*/pre_indexing.log +**/SalmonIndex/*/ref_indexing.log +**/SalmonIndex/*/seq.bin +**/dragmap/*/hash_table.cfg +**/dragmap/*/hash_table.cfg.bin +**/dragmap/*/hash_table_stats.txt .DS_Store multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 20e1bb87..5de4b219 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -28,6 +28,7 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -43,7 +44,6 @@ ], [ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", - "version0.51.1:md5,4adc522fa0fdaace79e45bcee7abb865", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] @@ -52,7 +52,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:37:47.995242455" + "timestamp": "2024-12-05T15:55:35.924356749" }, "Run with profile test for kallisto | --input assets/test/default_extended.yml": { "content": [ @@ -73,6 +73,7 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -85,7 +86,6 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "version0.51.1:md5,e425f39ad34d95970acdb16a706dfbb9", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], @@ -93,6 +93,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:37:21.239733377" + "timestamp": "2024-12-05T15:55:10.518283725" } } \ No newline at end of file From dc8efbbd4e090f5250d2d4f383b47cfc802bf4b1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 16:06:06 +0100 Subject: [PATCH 4/8] update snapshots --- tests/rnaseq.nf.test.snap | 3 +-- tests/rsem.nf.test.snap | 6 ++---- tests/salmon.nf.test.snap | 14 ++------------ tests/sarek.nf.test.snap | 5 +---- 4 files changed, 6 insertions(+), 22 deletions(-) diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index 9bd41e0d..4a80e0fe 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -96,7 +96,6 @@ "GRCh38_chr21.rev.1.ebwt:md5,5e5a45602d63d358e3edca7cdb683a1b", "GRCh38_chr21.rev.2.ebwt:md5,1e5088944137b3277e65306ea1a347a5", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", - "Log.out:md5,906d176b72e2bacef56c036a8c278644", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,1c9cd646313f1abb1cfc205ccab73464", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -120,6 +119,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:41:12.239111965" + "timestamp": "2024-12-05T15:59:30.460893418" } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 3a417e8e..61e61a86 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -57,7 +57,6 @@ [ "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", - "Log.out:md5,63ebdd9d823e1bc2929aa0ba93c995e1", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -86,7 +85,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:42:50.995387106" + "timestamp": "2024-12-05T16:01:13.352587524" }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ @@ -159,7 +158,6 @@ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", - "Log.out:md5,810ffedc0e26770f9b71923e55f55152", "SA:md5,074ae54177bb7b9cb981382f043f36e5", "SAindex:md5,81a04dbb4a8366c02907ad35218d877e", "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac", @@ -189,6 +187,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:44:39.234286812" + "timestamp": "2024-12-05T16:03:06.550798189" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 851fbc18..b1f1d1da 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -59,19 +59,14 @@ [ "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", - "ctable.bin:md5,365045f97860044295656c7cc8babf81", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", - "pos.bin:md5,388eac191e3fdf5c22b6b4c222e83de0", - "pre_indexing.log:md5,a44f369e65821a957131940c7741055c", "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", - "ref_indexing.log:md5,ee5a550ddededd200b63a2376bc59ca9", "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", - "seq.bin:md5,5d9e283968d9bcd0a766cff289d61d2f", "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" @@ -81,7 +76,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:46:46.179472015" + "timestamp": "2024-12-05T16:05:26.021361965" }, "Run with profile test for salmon | --input assets/test/default_extended.yml": { "content": [ @@ -130,19 +125,14 @@ ], [ "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", - "ctable.bin:md5,a5f381189da767e61e32a187459a5cce", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", "duplicate_clusters.tsv:md5,b65592e6f604234ac3cf45f8cafd8d27", "info.json:md5,e13f6500d048a7f72bcc385ce54bd50a", "mphf.bin:md5,9651ab954dccca304b6dcddf50fbae61", - "pos.bin:md5,ac2d0c717b65b7e93e7f1b289a4303c5", - "pre_indexing.log:md5,8011b3770d6ca53e60fbbe9fcbb0266d", "rank.bin:md5,e2ee4a817caa0614c7cfa732358aa829", "refAccumLengths.bin:md5,f79c13f67c09f87982ff1503826d6350", - "ref_indexing.log:md5,be29c64b496ce13846959ba4c0c1678d", "reflengths.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "refseq.bin:md5,dbe45319a08f3ea4b9eed98787b683ba", - "seq.bin:md5,c335689351bd0a27c3220ea1c5eafc65", "versionInfo.json:md5,d2c799050e81aa6e282ac8a73e773941", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] @@ -151,6 +141,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:45:46.523172582" + "timestamp": "2024-12-05T16:04:33.548164895" } } \ No newline at end of file diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap index fcc5c8a0..589e4540 100644 --- a/tests/sarek.nf.test.snap +++ b/tests/sarek.nf.test.snap @@ -102,10 +102,7 @@ "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070", "genome.dict:md5,2433fe2ba31257337bf4c4bd4cb8da15", "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685", - "hash_table.cfg:md5,9b55cf0e9be8b4afbcb80dcd1189293a", - "hash_table.cfg.bin:md5,111788e4f8f8e1745966a4f7d837e23b", "hash_table.cmp:md5,1caab4ffc89f81ace615a2e813295cf4", - "hash_table_stats.txt:md5,fd8b502fdd0fa8070cbf207dec8597af", "ref_index.bin:md5,dbb5c7d26b974e0ac338024fe4535044", "reference.bin:md5,be67b80ee48aa96b383fd72f1ccfefea", "repeat_mask.bin:md5,294939f1f80aa7f4a70b9b537e4c0f21", @@ -117,6 +114,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:48:02.521229914" + "timestamp": "2024-12-05T16:05:53.957141742" } } \ No newline at end of file From 2daacedf43ffa4d74b3664c9fa20aefcf3c23c1b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 18:36:46 +0100 Subject: [PATCH 5/8] alternate publishing solution --- main.nf | 10 +- modules.json | 9 +- .../nf-core/hisat2/build/hisat2-build.diff | 27 +++++ modules/nf-core/hisat2/build/main.nf | 3 +- .../kallisto/index/kallisto-index.diff | 27 +++++ modules/nf-core/kallisto/index/main.nf | 3 +- modules/nf-core/rsem/preparereference/main.nf | 3 +- .../rsem-preparereference.diff | 11 +- modules/nf-core/salmon/index/main.nf | 3 +- .../nf-core/salmon/index/salmon-index.diff | 10 +- modules/nf-core/star/genomegenerate/main.nf | 3 +- .../genomegenerate/star-genomegenerate.diff | 27 +++++ .../local/create_align_index_with_gff/main.nf | 2 +- tests/.nftignore | 14 +-- tests/hisat2.nf.test.snap | 42 +++---- tests/kallisto.nf.test.snap | 14 ++- tests/rnaseq.nf.test.snap | 37 +++--- tests/rsem.nf.test.snap | 106 +++++++++--------- tests/salmon.nf.test.snap | 70 ++++++------ 19 files changed, 266 insertions(+), 155 deletions(-) create mode 100644 modules/nf-core/hisat2/build/hisat2-build.diff create mode 100644 modules/nf-core/kallisto/index/kallisto-index.diff create mode 100644 modules/nf-core/star/genomegenerate/star-genomegenerate.diff diff --git a/main.nf b/main.nf index 632fc667..73483fda 100644 --- a/main.nf +++ b/main.nf @@ -133,13 +133,13 @@ output { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } } } 'hisat2_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/version2.2.1" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/${meta.source_gff}/version2.2.1" } } } 'intervals_bed' { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/intervals/${file}" } } } 'kallisto_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1/${file}" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/${meta.source_gff}/version0.51.1/${file}" } } } 'msisensorpro_list' { path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/msisensorpro/${file}" } } @@ -154,16 +154,16 @@ output { path { folder -> { file -> "multiqc/multiqc_report" } } } 'rsem_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/version1.3.1" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/${meta.source_gff}/version1.3.1" } } } 'salmon_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/version1.10.3" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/${meta.source_gff}/version1.10.3" } } } 'splice_sites' { path { meta, txt -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SpliceSites/${file}" } } } 'star_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/version2.7.11b" } } + path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/${meta.source_gff}/version2.7.11b" } } } 'transcript_fasta' { path { meta, fasta -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/TranscriptFasta/${file}" } } diff --git a/modules.json b/modules.json index a2e2b4ec..90c158c6 100644 --- a/modules.json +++ b/modules.json @@ -59,7 +59,8 @@ "hisat2/build": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/hisat2/build/hisat2-build.diff" }, "hisat2/extractsplicesites": { "branch": "master", @@ -69,7 +70,8 @@ "kallisto/index": { "branch": "master", "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/kallisto/index/kallisto-index.diff" }, "msisensorpro/scan": { "branch": "master", @@ -107,7 +109,8 @@ "star/genomegenerate": { "branch": "master", "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff" }, "tabix/tabix": { "branch": "master", diff --git a/modules/nf-core/hisat2/build/hisat2-build.diff b/modules/nf-core/hisat2/build/hisat2-build.diff new file mode 100644 index 00000000..2386242d --- /dev/null +++ b/modules/nf-core/hisat2/build/hisat2-build.diff @@ -0,0 +1,27 @@ +Changes in module 'nf-core/hisat2/build' +Changes in 'hisat2/build/main.nf': +--- modules/nf-core/hisat2/build/main.nf ++++ modules/nf-core/hisat2/build/main.nf +@@ -14,13 +14,14 @@ + tuple val(meta3), path(splicesites) + + output: +- tuple val(meta), path("hisat2") , emit: index ++ tuple val(meta_out), path("hisat2") , emit: index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: ++ meta_out = meta + [source_gff:gtf.baseName] + def args = task.ext.args ?: '' + def avail_mem = 0 + if (!task.memory) { + +'modules/nf-core/hisat2/build/meta.yml' is unchanged +'modules/nf-core/hisat2/build/environment.yml' is unchanged +'modules/nf-core/hisat2/build/tests/main.nf.test.snap' is unchanged +'modules/nf-core/hisat2/build/tests/main.nf.test' is unchanged +'modules/nf-core/hisat2/build/tests/tags.yml' is unchanged +************************************************************ diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 37a3e456..175c4535 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -14,13 +14,14 @@ process HISAT2_BUILD { tuple val(meta3), path(splicesites) output: - tuple val(meta), path("hisat2") , emit: index + tuple val(meta_out), path("hisat2") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def avail_mem = 0 if (!task.memory) { diff --git a/modules/nf-core/kallisto/index/kallisto-index.diff b/modules/nf-core/kallisto/index/kallisto-index.diff new file mode 100644 index 00000000..8b51bc2c --- /dev/null +++ b/modules/nf-core/kallisto/index/kallisto-index.diff @@ -0,0 +1,27 @@ +Changes in module 'nf-core/kallisto/index' +Changes in 'kallisto/index/main.nf': +--- modules/nf-core/kallisto/index/main.nf ++++ modules/nf-core/kallisto/index/main.nf +@@ -11,13 +11,14 @@ + tuple val(meta), path(fasta) + + output: +- tuple val(meta), path("kallisto") , emit: index ++ tuple val(meta_out), path("kallisto") , emit: index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: ++ meta_out = meta + [source_gff:fasta.baseName] + def args = task.ext.args ?: '' + """ + kallisto \\ + +'modules/nf-core/kallisto/index/meta.yml' is unchanged +'modules/nf-core/kallisto/index/environment.yml' is unchanged +'modules/nf-core/kallisto/index/tests/main.nf.test.snap' is unchanged +'modules/nf-core/kallisto/index/tests/main.nf.test' is unchanged +'modules/nf-core/kallisto/index/tests/tags.yml' is unchanged +************************************************************ diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 73a5f7a9..77a207b9 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -11,13 +11,14 @@ process KALLISTO_INDEX { tuple val(meta), path(fasta) output: - tuple val(meta), path("kallisto") , emit: index + tuple val(meta_out), path("kallisto") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + meta_out = meta + [source_gff:fasta.baseName] def args = task.ext.args ?: '' """ kallisto \\ diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index b2d961a2..b15322c1 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -12,7 +12,7 @@ process RSEM_PREPAREREFERENCE { tuple val(meta2), path(gtf) output: - tuple val(meta), path("rsem") , emit: index + tuple val(meta_out), path("rsem") , emit: index tuple val(meta), path("*transcripts.fa"), emit: transcript_fasta path "versions.yml" , emit: versions @@ -20,6 +20,7 @@ process RSEM_PREPAREREFERENCE { task.ext.when == null || task.ext.when script: + meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args_list = args.tokenize() diff --git a/modules/nf-core/rsem/preparereference/rsem-preparereference.diff b/modules/nf-core/rsem/preparereference/rsem-preparereference.diff index 5a76d532..1ad8c160 100644 --- a/modules/nf-core/rsem/preparereference/rsem-preparereference.diff +++ b/modules/nf-core/rsem/preparereference/rsem-preparereference.diff @@ -2,7 +2,7 @@ Changes in module 'nf-core/rsem/preparereference' Changes in 'rsem/preparereference/main.nf': --- modules/nf-core/rsem/preparereference/main.nf +++ modules/nf-core/rsem/preparereference/main.nf -@@ -8,12 +8,12 @@ +@@ -8,18 +8,19 @@ 'biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" input: @@ -14,11 +14,18 @@ Changes in 'rsem/preparereference/main.nf': output: - path "rsem" , emit: index - path "*transcripts.fa", emit: transcript_fasta -+ tuple val(meta), path("rsem") , emit: index ++ tuple val(meta_out), path("rsem") , emit: index + tuple val(meta), path("*transcripts.fa"), emit: transcript_fasta path "versions.yml" , emit: versions when: + task.ext.when == null || task.ext.when + + script: ++ meta_out = meta + [source_gff:gtf.baseName] + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args_list = args.tokenize() 'modules/nf-core/rsem/preparereference/meta.yml' is unchanged 'modules/nf-core/rsem/preparereference/environment.yml' is unchanged diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 24803ddf..1d0ebb04 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -12,13 +12,14 @@ process SALMON_INDEX { tuple val(meta2), path(transcript_fasta) output: - tuple val(meta), path("salmon"), emit: index + tuple val(meta_out), path("salmon"), emit: index path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: + meta_out = meta + [source_gff:transcript_fasta.baseName] def args = task.ext.args ?: '' def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt" def gentrome = "gentrome.fa" diff --git a/modules/nf-core/salmon/index/salmon-index.diff b/modules/nf-core/salmon/index/salmon-index.diff index 45e7b015..6d39a33e 100644 --- a/modules/nf-core/salmon/index/salmon-index.diff +++ b/modules/nf-core/salmon/index/salmon-index.diff @@ -2,7 +2,7 @@ Changes in module 'nf-core/salmon/index' Changes in 'salmon/index/main.nf': --- modules/nf-core/salmon/index/main.nf +++ modules/nf-core/salmon/index/main.nf -@@ -8,12 +8,12 @@ +@@ -8,17 +8,18 @@ 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: @@ -14,11 +14,17 @@ Changes in 'salmon/index/main.nf': output: - path "salmon" , emit: index - path "versions.yml", emit: versions -+ tuple val(meta), path("salmon"), emit: index ++ tuple val(meta_out), path("salmon"), emit: index + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when + + script: ++ meta_out = meta + [source_gff:transcript_fasta.baseName] + def args = task.ext.args ?: '' + def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt" + def gentrome = "gentrome.fa" 'modules/nf-core/salmon/index/meta.yml' is unchanged 'modules/nf-core/salmon/index/environment.yml' is unchanged diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 8f0c67e7..04f0aa49 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -12,13 +12,14 @@ process STAR_GENOMEGENERATE { tuple val(meta2), path(gtf) output: - tuple val(meta), path("star") , emit: index + tuple val(meta_out), path("star") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def args_list = args.tokenize() def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff new file mode 100644 index 00000000..05666e7d --- /dev/null +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -0,0 +1,27 @@ +Changes in module 'nf-core/star/genomegenerate' +Changes in 'star/genomegenerate/main.nf': +--- modules/nf-core/star/genomegenerate/main.nf ++++ modules/nf-core/star/genomegenerate/main.nf +@@ -12,13 +12,14 @@ + tuple val(meta2), path(gtf) + + output: +- tuple val(meta), path("star") , emit: index ++ tuple val(meta_out), path("star") , emit: index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: ++ meta_out = meta + [source_gff:gtf.baseName] + def args = task.ext.args ?: '' + def args_list = args.tokenize() + def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + +'modules/nf-core/star/genomegenerate/meta.yml' is unchanged +'modules/nf-core/star/genomegenerate/environment.yml' is unchanged +'modules/nf-core/star/genomegenerate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/star/genomegenerate/tests/main.nf.test' is unchanged +'modules/nf-core/star/genomegenerate/tests/tags.yml' is unchanged +************************************************************ diff --git a/subworkflows/local/create_align_index_with_gff/main.nf b/subworkflows/local/create_align_index_with_gff/main.nf index 0ca28be4..465d81ee 100644 --- a/subworkflows/local/create_align_index_with_gff/main.nf +++ b/subworkflows/local/create_align_index_with_gff/main.nf @@ -57,6 +57,7 @@ workflow CREATE_ALIGN_INDEX_WITH_GFF { HISAT2_EXTRACTSPLICESITES(gtf_hisat2) + versions = versions.mix(HISAT2_EXTRACTSPLICESITES.out.versions) splice_sites = input_splice_sites.mix(HISAT2_EXTRACTSPLICESITES.out.txt) if (run_hisat2) { @@ -68,7 +69,6 @@ workflow CREATE_ALIGN_INDEX_WITH_GFF { hisat2_index = HISAT2_BUILD.out.index - versions = versions.mix(HISAT2_EXTRACTSPLICESITES.out.versions) versions = versions.mix(HISAT2_BUILD.out.versions) } } diff --git a/tests/.nftignore b/tests/.nftignore index 94dd6057..9bd0a0d1 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,11 +1,11 @@ **/kallisto -**/RSEMIndex/*/Log.out -**/STARIndex/*/Log.out -**/SalmonIndex/*/ctable.bin -**/SalmonIndex/*/pos.bin -**/SalmonIndex/*/pre_indexing.log -**/SalmonIndex/*/ref_indexing.log -**/SalmonIndex/*/seq.bin +**/RSEMIndex/**/Log.out +**/STARIndex/**/Log.out +**/SalmonIndex/**/ctable.bin +**/SalmonIndex/**/pos.bin +**/SalmonIndex/**/pre_indexing.log +**/SalmonIndex/**/ref_indexing.log +**/SalmonIndex/**/seq.bin **/dragmap/*/hash_table.cfg **/dragmap/*/hash_table.cfg.bin **/dragmap/*/hash_table_stats.txt diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 6f641664..9b466c0e 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -17,15 +17,16 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.8.ht2", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -53,7 +54,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:35:30.36657085" + "timestamp": "2024-12-05T17:50:52.053323321" }, "Run with profile test for hisat2 | --input GRCh38_chr21.yml": { "content": [ @@ -82,15 +83,16 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.8.ht2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites/GRCh38_chr21.splice_sites.txt", "multiqc", @@ -122,6 +124,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:36:59.914837757" + "timestamp": "2024-12-05T17:52:28.323161796" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 5de4b219..08197842 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -27,8 +27,9 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1/kallisto", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -52,7 +53,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:55:35.924356749" + "timestamp": "2024-12-05T17:53:22.223391773" }, "Run with profile test for kallisto | --input assets/test/default_extended.yml": { "content": [ @@ -72,8 +73,9 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1/kallisto", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -93,6 +95,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:55:10.518283725" + "timestamp": "2024-12-05T17:52:47.903698539" } } \ No newline at end of file diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index 4a80e0fe..91b61f6e 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -50,23 +50,24 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.1.ebwt", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.2.ebwt", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.fai", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.sizes", @@ -119,6 +120,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T15:59:30.460893418" + "timestamp": "2024-12-05T18:10:34.850065075" } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 61e61a86..1bff183d 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -18,31 +18,32 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/transcriptInfo.tab", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -85,7 +86,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T16:01:13.352587524" + "timestamp": "2024-12-05T18:12:25.831925672" }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ @@ -116,31 +117,32 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -187,6 +189,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T16:03:06.550798189" + "timestamp": "2024-12-05T18:14:26.209320615" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index b1f1d1da..e9671869 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -27,22 +27,23 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/versionInfo.json", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -76,7 +77,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T16:05:26.021361965" + "timestamp": "2024-12-05T18:16:38.328916577" }, "Run with profile test for salmon | --input assets/test/default_extended.yml": { "content": [ @@ -96,22 +97,23 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/versionInfo.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -141,6 +143,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T16:04:33.548164895" + "timestamp": "2024-12-05T18:15:45.201097223" } } \ No newline at end of file From 26fcce5de4013cd31c5106536a1b8249986a168c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 5 Dec 2024 19:38:09 +0100 Subject: [PATCH 6/8] properly fix merge conflicts --- tests/hisat2.nf.test.snap | 20 -------------------- tests/kallisto.nf.test.snap | 13 ------------- tests/rnaseq.nf.test.snap | 4 ---- tests/rsem.nf.test.snap | 36 ------------------------------------ tests/salmon.nf.test.snap | 27 --------------------------- tests/samtools.nf.test.snap | 2 +- 6 files changed, 1 insertion(+), 101 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 199ca832..bd14e829 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -54,11 +54,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T17:50:52.053323321" -======= - "timestamp": "2024-12-05T15:35:30.36657085" ->>>>>>> dev }, "Run with profile test for hisat2 | --input GRCh38_chr21.yml": { "content": [ @@ -87,7 +83,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", -<<<<<<< HEAD "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.1.ht2", @@ -98,17 +93,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.6.ht2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.7.ht2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.8.ht2", -======= - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", ->>>>>>> dev "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites/GRCh38_chr21.splice_sites.txt", "multiqc", @@ -140,10 +124,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T17:52:28.323161796" -======= - "timestamp": "2024-12-05T15:36:59.914837757" ->>>>>>> dev } } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 42209462..4ceb037f 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -53,11 +53,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T17:53:22.223391773" -======= - "timestamp": "2024-12-05T15:55:35.924356749" ->>>>>>> dev }, "Run with profile test for kallisto | --input assets/test/default_extended.yml": { "content": [ @@ -77,14 +73,9 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", -<<<<<<< HEAD "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1/kallisto", -======= - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", ->>>>>>> dev "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -104,10 +95,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T17:52:47.903698539" -======= - "timestamp": "2024-12-05T15:55:10.518283725" ->>>>>>> dev } } diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index d2813dfa..b600a282 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -120,10 +120,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T18:10:34.850065075" -======= - "timestamp": "2024-12-05T15:59:30.460893418" ->>>>>>> dev } } diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index a5504c2f..3803cc5d 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -86,11 +86,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T18:12:25.831925672" -======= - "timestamp": "2024-12-05T16:01:13.352587524" ->>>>>>> dev }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ @@ -121,7 +117,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", -<<<<<<< HEAD "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/GRCh38_chr21.fa", @@ -148,33 +143,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.fromGTF.out.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.out.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/transcriptInfo.tab", -======= - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", ->>>>>>> dev "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -221,10 +189,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T18:14:26.209320615" -======= - "timestamp": "2024-12-05T16:03:06.550798189" ->>>>>>> dev } } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 9569c7c5..78363c5f 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -77,11 +77,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T18:16:38.328916577" -======= - "timestamp": "2024-12-05T16:05:26.021361965" ->>>>>>> dev }, "Run with profile test for salmon | --input assets/test/default_extended.yml": { "content": [ @@ -101,7 +97,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", -<<<<<<< HEAD "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/complete_ref_lens.bin", @@ -119,24 +114,6 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refseq.bin", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/seq.bin", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/versionInfo.json", -======= - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", ->>>>>>> dev "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -166,10 +143,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, -<<<<<<< HEAD "timestamp": "2024-12-05T18:15:45.201097223" -======= - "timestamp": "2024-12-05T16:04:33.548164895" ->>>>>>> dev } } diff --git a/tests/samtools.nf.test.snap b/tests/samtools.nf.test.snap index a2424ae4..dfdca6ff 100644 --- a/tests/samtools.nf.test.snap +++ b/tests/samtools.nf.test.snap @@ -120,4 +120,4 @@ }, "timestamp": "2024-11-28T14:47:38.70092941" } -} \ No newline at end of file +} From ad57aa3fa720150323ed3cff02a05b8c3997c90b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 6 Dec 2024 11:59:31 +0100 Subject: [PATCH 7/8] simplify source_gff --- assets/schema_input.json | 7 ++ assets/test/default_extended.yml | 1 + main.nf | 40 ++++++- .../nf-core/hisat2/build/hisat2-build.diff | 27 ----- modules/nf-core/hisat2/build/main.nf | 3 +- .../kallisto/index/kallisto-index.diff | 27 ----- modules/nf-core/kallisto/index/main.nf | 3 +- modules/nf-core/rsem/preparereference/main.nf | 3 +- .../rsem-preparereference.diff | 11 +- modules/nf-core/salmon/index/main.nf | 3 +- .../nf-core/salmon/index/salmon-index.diff | 10 +- modules/nf-core/star/genomegenerate/main.nf | 3 +- .../genomegenerate/star-genomegenerate.diff | 27 ----- tests/hisat2.nf.test.snap | 45 ++++---- tests/kallisto.nf.test.snap | 17 ++- tests/rnaseq.nf.test.snap | 39 +++---- tests/rsem.nf.test.snap | 109 +++++++++--------- tests/salmon.nf.test.snap | 73 ++++++------ 18 files changed, 191 insertions(+), 257 deletions(-) delete mode 100644 modules/nf-core/hisat2/build/hisat2-build.diff delete mode 100644 modules/nf-core/kallisto/index/kallisto-index.diff delete mode 100644 modules/nf-core/star/genomegenerate/star-genomegenerate.diff diff --git a/assets/schema_input.json b/assets/schema_input.json index 784a8827..3528ad42 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -21,8 +21,15 @@ "source_vcf": { "type": "string", "errorMessage": "Where the references came from", + "default": "unknown", "meta": ["source_vcf"] }, + "source_gff": { + "type": "string", + "errorMessage": "Where the references came from", + "default": "unknown", + "meta": ["source_gff"] + }, "species": { "type": "string", "errorMessage": "Species of the reference", diff --git a/assets/test/default_extended.yml b/assets/test/default_extended.yml index a51628b3..e290e6aa 100644 --- a/assets/test/default_extended.yml +++ b/assets/test/default_extended.yml @@ -5,6 +5,7 @@ fasta_sizes: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.sizes" gff: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gff" gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf" + source_gff: "CUSTOM" mito_name: "MT" readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md" source: "nf-core/references" diff --git a/main.nf b/main.nf index 73483fda..2112566d 100644 --- a/main.nf +++ b/main.nf @@ -133,13 +133,25 @@ output { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } } } 'hisat2_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/${meta.source_gff}/version2.2.1" } } + path { meta, index -> + { file -> + meta.source_gff == "unknown" + ? "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/version2.2.1" + : "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/${meta.source_gff}/version2.2.1" + } + } } 'intervals_bed' { path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/intervals/${file}" } } } 'kallisto_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/${meta.source_gff}/version0.51.1/${file}" } } + path { meta, index -> + { file -> + meta.source_gff == "unknown" + ? "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1/${file}" + : "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/${meta.source_gff}/version0.51.1/${file}" + } + } } 'msisensorpro_list' { path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/msisensorpro/${file}" } } @@ -154,16 +166,34 @@ output { path { folder -> { file -> "multiqc/multiqc_report" } } } 'rsem_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/${meta.source_gff}/version1.3.1" } } + path { meta, index -> + { file -> + meta.source_gff == "unknown" + ? "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/version1.3.1" + : "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/${meta.source_gff}/version1.3.1" + } + } } 'salmon_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/${meta.source_gff}/version1.10.3" } } + path { meta, index -> + { file -> + meta.source_gff == "unknown" + ? "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/version1.10.3" + : "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/${meta.source_gff}/version1.10.3" + } + } } 'splice_sites' { path { meta, txt -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SpliceSites/${file}" } } } 'star_index' { - path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/${meta.source_gff}/version2.7.11b" } } + path { meta, index -> + { file -> + meta.source_gff == "unknown" + ? "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/version2.7.11b" + : "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/${meta.source_gff}/version2.7.11b" + } + } } 'transcript_fasta' { path { meta, fasta -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/TranscriptFasta/${file}" } } diff --git a/modules/nf-core/hisat2/build/hisat2-build.diff b/modules/nf-core/hisat2/build/hisat2-build.diff deleted file mode 100644 index 2386242d..00000000 --- a/modules/nf-core/hisat2/build/hisat2-build.diff +++ /dev/null @@ -1,27 +0,0 @@ -Changes in module 'nf-core/hisat2/build' -Changes in 'hisat2/build/main.nf': ---- modules/nf-core/hisat2/build/main.nf -+++ modules/nf-core/hisat2/build/main.nf -@@ -14,13 +14,14 @@ - tuple val(meta3), path(splicesites) - - output: -- tuple val(meta), path("hisat2") , emit: index -+ tuple val(meta_out), path("hisat2") , emit: index - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: -+ meta_out = meta + [source_gff:gtf.baseName] - def args = task.ext.args ?: '' - def avail_mem = 0 - if (!task.memory) { - -'modules/nf-core/hisat2/build/meta.yml' is unchanged -'modules/nf-core/hisat2/build/environment.yml' is unchanged -'modules/nf-core/hisat2/build/tests/main.nf.test.snap' is unchanged -'modules/nf-core/hisat2/build/tests/main.nf.test' is unchanged -'modules/nf-core/hisat2/build/tests/tags.yml' is unchanged -************************************************************ diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 175c4535..37a3e456 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -14,14 +14,13 @@ process HISAT2_BUILD { tuple val(meta3), path(splicesites) output: - tuple val(meta_out), path("hisat2") , emit: index + tuple val(meta), path("hisat2") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def avail_mem = 0 if (!task.memory) { diff --git a/modules/nf-core/kallisto/index/kallisto-index.diff b/modules/nf-core/kallisto/index/kallisto-index.diff deleted file mode 100644 index 8b51bc2c..00000000 --- a/modules/nf-core/kallisto/index/kallisto-index.diff +++ /dev/null @@ -1,27 +0,0 @@ -Changes in module 'nf-core/kallisto/index' -Changes in 'kallisto/index/main.nf': ---- modules/nf-core/kallisto/index/main.nf -+++ modules/nf-core/kallisto/index/main.nf -@@ -11,13 +11,14 @@ - tuple val(meta), path(fasta) - - output: -- tuple val(meta), path("kallisto") , emit: index -+ tuple val(meta_out), path("kallisto") , emit: index - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: -+ meta_out = meta + [source_gff:fasta.baseName] - def args = task.ext.args ?: '' - """ - kallisto \\ - -'modules/nf-core/kallisto/index/meta.yml' is unchanged -'modules/nf-core/kallisto/index/environment.yml' is unchanged -'modules/nf-core/kallisto/index/tests/main.nf.test.snap' is unchanged -'modules/nf-core/kallisto/index/tests/main.nf.test' is unchanged -'modules/nf-core/kallisto/index/tests/tags.yml' is unchanged -************************************************************ diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 77a207b9..73a5f7a9 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -11,14 +11,13 @@ process KALLISTO_INDEX { tuple val(meta), path(fasta) output: - tuple val(meta_out), path("kallisto") , emit: index + tuple val(meta), path("kallisto") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - meta_out = meta + [source_gff:fasta.baseName] def args = task.ext.args ?: '' """ kallisto \\ diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index b15322c1..b2d961a2 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -12,7 +12,7 @@ process RSEM_PREPAREREFERENCE { tuple val(meta2), path(gtf) output: - tuple val(meta_out), path("rsem") , emit: index + tuple val(meta), path("rsem") , emit: index tuple val(meta), path("*transcripts.fa"), emit: transcript_fasta path "versions.yml" , emit: versions @@ -20,7 +20,6 @@ process RSEM_PREPAREREFERENCE { task.ext.when == null || task.ext.when script: - meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args_list = args.tokenize() diff --git a/modules/nf-core/rsem/preparereference/rsem-preparereference.diff b/modules/nf-core/rsem/preparereference/rsem-preparereference.diff index 1ad8c160..5a76d532 100644 --- a/modules/nf-core/rsem/preparereference/rsem-preparereference.diff +++ b/modules/nf-core/rsem/preparereference/rsem-preparereference.diff @@ -2,7 +2,7 @@ Changes in module 'nf-core/rsem/preparereference' Changes in 'rsem/preparereference/main.nf': --- modules/nf-core/rsem/preparereference/main.nf +++ modules/nf-core/rsem/preparereference/main.nf -@@ -8,18 +8,19 @@ +@@ -8,12 +8,12 @@ 'biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" input: @@ -14,18 +14,11 @@ Changes in 'rsem/preparereference/main.nf': output: - path "rsem" , emit: index - path "*transcripts.fa", emit: transcript_fasta -+ tuple val(meta_out), path("rsem") , emit: index ++ tuple val(meta), path("rsem") , emit: index + tuple val(meta), path("*transcripts.fa"), emit: transcript_fasta path "versions.yml" , emit: versions when: - task.ext.when == null || task.ext.when - - script: -+ meta_out = meta + [source_gff:gtf.baseName] - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' - def args_list = args.tokenize() 'modules/nf-core/rsem/preparereference/meta.yml' is unchanged 'modules/nf-core/rsem/preparereference/environment.yml' is unchanged diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 1d0ebb04..24803ddf 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -12,14 +12,13 @@ process SALMON_INDEX { tuple val(meta2), path(transcript_fasta) output: - tuple val(meta_out), path("salmon"), emit: index + tuple val(meta), path("salmon"), emit: index path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - meta_out = meta + [source_gff:transcript_fasta.baseName] def args = task.ext.args ?: '' def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt" def gentrome = "gentrome.fa" diff --git a/modules/nf-core/salmon/index/salmon-index.diff b/modules/nf-core/salmon/index/salmon-index.diff index 6d39a33e..45e7b015 100644 --- a/modules/nf-core/salmon/index/salmon-index.diff +++ b/modules/nf-core/salmon/index/salmon-index.diff @@ -2,7 +2,7 @@ Changes in module 'nf-core/salmon/index' Changes in 'salmon/index/main.nf': --- modules/nf-core/salmon/index/main.nf +++ modules/nf-core/salmon/index/main.nf -@@ -8,17 +8,18 @@ +@@ -8,12 +8,12 @@ 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: @@ -14,17 +14,11 @@ Changes in 'salmon/index/main.nf': output: - path "salmon" , emit: index - path "versions.yml", emit: versions -+ tuple val(meta_out), path("salmon"), emit: index ++ tuple val(meta), path("salmon"), emit: index + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when - - script: -+ meta_out = meta + [source_gff:transcript_fasta.baseName] - def args = task.ext.args ?: '' - def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 | cut -d \$'\\t' -f 1 > decoys.txt" - def gentrome = "gentrome.fa" 'modules/nf-core/salmon/index/meta.yml' is unchanged 'modules/nf-core/salmon/index/environment.yml' is unchanged diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 04f0aa49..8f0c67e7 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -12,14 +12,13 @@ process STAR_GENOMEGENERATE { tuple val(meta2), path(gtf) output: - tuple val(meta_out), path("star") , emit: index + tuple val(meta), path("star") , emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - meta_out = meta + [source_gff:gtf.baseName] def args = task.ext.args ?: '' def args_list = args.tokenize() def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff deleted file mode 100644 index 05666e7d..00000000 --- a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff +++ /dev/null @@ -1,27 +0,0 @@ -Changes in module 'nf-core/star/genomegenerate' -Changes in 'star/genomegenerate/main.nf': ---- modules/nf-core/star/genomegenerate/main.nf -+++ modules/nf-core/star/genomegenerate/main.nf -@@ -12,13 +12,14 @@ - tuple val(meta2), path(gtf) - - output: -- tuple val(meta), path("star") , emit: index -+ tuple val(meta_out), path("star") , emit: index - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: -+ meta_out = meta + [source_gff:gtf.baseName] - def args = task.ext.args ?: '' - def args_list = args.tokenize() - def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' - -'modules/nf-core/star/genomegenerate/meta.yml' is unchanged -'modules/nf-core/star/genomegenerate/environment.yml' is unchanged -'modules/nf-core/star/genomegenerate/tests/main.nf.test.snap' is unchanged -'modules/nf-core/star/genomegenerate/tests/main.nf.test' is unchanged -'modules/nf-core/star/genomegenerate/tests/tags.yml' is unchanged -************************************************************ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index bd14e829..cd3ebb81 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -17,16 +17,16 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/CUSTOM/version2.2.1/GRCh38_chr21.8.ht2", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -54,7 +54,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T17:50:52.053323321" + "timestamp": "2024-12-06T11:47:41.58238436" }, "Run with profile test for hisat2 | --input GRCh38_chr21.yml": { "content": [ @@ -83,16 +83,15 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.1.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.2.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.3.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.4.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.5.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.6.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.7.ht2", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21/version2.2.1/GRCh38_chr21.8.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.1.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.2.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.3.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.4.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.5.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.6.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.7.ht2", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/version2.2.1/GRCh38_chr21.8.ht2", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites/GRCh38_chr21.splice_sites.txt", "multiqc", @@ -124,6 +123,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T17:52:28.323161796" + "timestamp": "2024-12-06T11:33:17.476760832" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 4ceb037f..8e4d8083 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -27,9 +27,8 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1/kallisto", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/version0.51.1/kallisto", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -53,7 +52,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T17:53:22.223391773" + "timestamp": "2024-12-06T11:34:03.486585563" }, "Run with profile test for kallisto | --input assets/test/default_extended.yml": { "content": [ @@ -73,9 +72,9 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/genome.transcripts/version0.51.1/kallisto", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/version0.51.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex/CUSTOM/version0.51.1/kallisto", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -95,6 +94,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T17:52:47.903698539" + "timestamp": "2024-12-06T11:50:22.597389596" } -} +} \ No newline at end of file diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index b600a282..90c20df0 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -50,24 +50,23 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.1.ebwt", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/BowtieIndex/version1.3.1/GRCh38_chr21.rev.2.ebwt", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/GRCh38_chr21/version2.7.11b/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/STARIndex/version2.7.11b/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.fai", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/WholeGenomeFasta/GRCh38_chr21.fa.sizes", @@ -120,6 +119,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T18:10:34.850065075" + "timestamp": "2024-12-06T11:37:48.115918724" } -} +} \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 3803cc5d..d7912587 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -18,32 +18,32 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/CUSTOM/version1.3.1/transcriptInfo.tab", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -86,7 +86,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T18:12:25.831925672" + "timestamp": "2024-12-06T11:54:36.556736231" }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ @@ -117,32 +117,31 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/GRCh38_chr21.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Genome", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/Log.out", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SA", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/SAindex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrName.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrNameLength.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/chrStart.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonGeTrInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/exonInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/geneInfo.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.chrlist", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.grp", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.n2g.idx.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.seq", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.ti", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genome.transcripts.fa", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/genomeParameters.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbInfo.txt", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.fromGTF.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/sjdbList.out.tab", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/GRCh38_chr21/version1.3.1/transcriptInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/GRCh38_chr21.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Genome", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/Log.out", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SA", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/SAindex", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrName.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrNameLength.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/chrStart.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonGeTrInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/exonInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/geneInfo.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.chrlist", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.grp", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.n2g.idx.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.seq", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.ti", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genome.transcripts.fa", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/genomeParameters.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbInfo.txt", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.fromGTF.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/sjdbList.out.tab", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/RSEMIndex/version1.3.1/transcriptInfo.tab", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -189,6 +188,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T18:14:26.209320615" + "timestamp": "2024-12-06T11:41:35.396864169" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 78363c5f..99988322 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -27,23 +27,22 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/version1.10.3/versionInfo.json", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa", "multiqc", @@ -77,7 +76,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T18:16:38.328916577" + "timestamp": "2024-12-06T11:43:27.413672277" }, "Run with profile test for salmon | --input assets/test/default_extended.yml": { "content": [ @@ -97,23 +96,23 @@ "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence", "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/complete_ref_lens.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctable.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ctg_offsets.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/duplicate_clusters.tsv", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/info.json", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/mphf.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pos.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/pre_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/rank.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refAccumLengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/ref_indexing.log", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/reflengths.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/refseq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/seq.bin", - "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/genome.transcripts/version1.10.3/versionInfo.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/complete_ref_lens.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/ctable.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/ctg_offsets.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/duplicate_clusters.tsv", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/info.json", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/mphf.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/pos.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/pre_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/rank.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/refAccumLengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/ref_indexing.log", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/reflengths.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/refseq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/seq.bin", + "Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SalmonIndex/CUSTOM/version1.10.3/versionInfo.json", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -143,6 +142,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T18:15:45.201097223" + "timestamp": "2024-12-06T11:57:24.351180092" } -} +} \ No newline at end of file From 5fa14dc8061af3cd3c1608674ad68562c94b7a72 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 6 Dec 2024 12:00:59 +0100 Subject: [PATCH 8/8] Update samtools.nf.test.snap