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Final publish extended #54

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merged 9 commits into from
Dec 6, 2024
Merged

Final publish extended #54

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e3bfb28
update CHANGELOG
maxulysse Dec 5, 2024
61150cf
Better publishing for all aligner indexes
maxulysse Dec 5, 2024
a105b53
fix kallisto
maxulysse Dec 5, 2024
dc8efbb
update snapshots
maxulysse Dec 5, 2024
2daaced
alternate publishing solution
maxulysse Dec 5, 2024
2b8abf4
Merge branch 'dev' into final_publish_extended
maxulysse Dec 5, 2024
26fcce5
properly fix merge conflicts
maxulysse Dec 5, 2024
ad57aa3
simplify source_gff
maxulysse Dec 6, 2024
5fa14dc
Update samtools.nf.test.snap
maxulysse Dec 6, 2024
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7 changes: 7 additions & 0 deletions assets/schema_input.json
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Expand Up @@ -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",
Expand Down
1 change: 1 addition & 0 deletions assets/test/default_extended.yml
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Expand Up @@ -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"
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40 changes: 35 additions & 5 deletions main.nf
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Expand Up @@ -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}/${meta.id}/Sequence/Hisat2Index/version2.2.1" } }
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
? "${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"
Comment on lines +138 to +140
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In the pipeline, do you add the name of the GFF to the meta map? This way we get this field populated by default:

meta = meta + [ "source_gff": ${gff.simpleName} ]

}
}
}
'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.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/${file}" } }
Expand All @@ -154,16 +166,34 @@ output {
path { folder -> { file -> "multiqc/multiqc_report" } }
}
'rsem_index' {
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/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/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/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}" } }
Expand Down
9 changes: 6 additions & 3 deletions modules.json
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Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/create_align_index_with_gff/main.nf
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Expand Up @@ -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) {
Expand All @@ -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)
}
}
Expand Down
14 changes: 7 additions & 7 deletions tests/.nftignore
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@@ -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
Expand Down
23 changes: 12 additions & 11 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -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/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",
Expand Down Expand Up @@ -53,7 +54,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T15:35:30.36657085"
"timestamp": "2024-12-06T11:47:41.58238436"
},
"Run with profile test for hisat2 | --input GRCh38_chr21.yml": {
"content": [
Expand Down Expand Up @@ -122,6 +123,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T15:36:59.914837757"
"timestamp": "2024-12-06T11:33:17.476760832"
}
}
9 changes: 5 additions & 4 deletions tests/kallisto.nf.test.snap
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Expand Up @@ -52,7 +52,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T15:55:35.924356749"
"timestamp": "2024-12-06T11:34:03.486585563"
},
"Run with profile test for kallisto | --input assets/test/default_extended.yml": {
"content": [
Expand All @@ -72,8 +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/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/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",
Expand All @@ -93,6 +94,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T15:55:10.518283725"
"timestamp": "2024-12-06T11:50:22.597389596"
}
}
2 changes: 1 addition & 1 deletion tests/rnaseq.nf.test.snap
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Expand Up @@ -119,6 +119,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T15:59:30.460893418"
"timestamp": "2024-12-06T11:37:48.115918724"
}
}
55 changes: 28 additions & 27 deletions tests/rsem.nf.test.snap
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Expand Up @@ -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/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",
Expand Down Expand Up @@ -85,7 +86,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T16:01:13.352587524"
"timestamp": "2024-12-06T11:54:36.556736231"
},
"Run with profile test for rsem | --input GRCh38_chr21.yml": {
"content": [
Expand Down Expand Up @@ -187,6 +188,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T16:03:06.550798189"
"timestamp": "2024-12-06T11:41:35.396864169"
}
}
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