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Merge pull request #459 from atrigila/fix_linting
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Update modules and subworkflows, fix linting
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@atrigila
atrigila authored Oct 2, 2024
2 parents 4c64d73 + 644515c commit b0be55f
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#448]](https://github.com/nf-core/smrnaseq/pull/448) - Migrate local mirdeep to [nf-core mirdeep2 modules and subworkflow](https://github.com/nf-core/smrnaseq/issues/443) and generate [test profile for mirdeep2](https://github.com/nf-core/smrnaseq/issues/399).
- [[#452]](https://github.com/nf-core/smrnaseq/pull/452) - Fix [Fix ch_bowtie_index channel structure](https://github.com/nf-core/smrnaseq/issues/451) and replace untarfiles with untar [replace untarfiles with untar](https://github.com/nf-core/smrnaseq/issues/449).
- [[#457]](https://github.com/nf-core/smrnaseq/pull/457) - QC all input [fasta files and clean them](https://github.com/nf-core/smrnaseq/issues/455).
- [[#459]](https://github.com/nf-core/smrnaseq/pull/459) - Update modules and subworkflows [and fix linting](https://github.com/nf-core/smrnaseq/issues/458).

## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

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44 changes: 22 additions & 22 deletions modules.json
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Expand Up @@ -7,13 +7,13 @@
"nf-core": {
"bioawk": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/bioawk/bioawk.diff"
},
"blat": {
"branch": "master",
"git_sha": "49852039cccef84bbf5a3c0e069fac81fa3f0202",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bowtie/align": {
Expand All @@ -23,7 +23,7 @@
},
"bowtie/build": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bowtie2/align": {
Expand All @@ -33,12 +33,12 @@
},
"bowtie2/build": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"cat/fastq": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"csvtk/join": {
Expand All @@ -48,22 +48,22 @@
},
"fastp": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"gawk": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"mirdeep2/mapper": {
"branch": "master",
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"git_sha": "26757a6a54d05c3133c01c564c192ff617c5ea33",
"installed_by": ["fastq_find_mirna_mirdeep2"]
},
"mirdeep2/mirdeep2": {
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},
"mirtrace/qc": {
"branch": "master",
"git_sha": "6dd363c9b9b7cf30c4418597d20b6861848f0475",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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},
"multiqc": {
"branch": "master",
"git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_sort_stats_samtools", "modules"]
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_sort_stats_samtools", "modules"]
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"samtools/stats": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools", "modules"]
},
"seqcluster/collapse": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"seqkit/fq2fa": {
Expand All @@ -138,7 +138,7 @@
},
"seqkit/grep": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/seqkit/grep/seqkit-grep.diff"
},
Expand All @@ -149,12 +149,12 @@
},
"umicollapse": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"umitools/extract": {
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"untar": {
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},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
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"git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
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53 changes: 29 additions & 24 deletions modules/nf-core/bioawk/meta.yml
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67 changes: 35 additions & 32 deletions modules/nf-core/blat/meta.yml
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41 changes: 22 additions & 19 deletions modules/nf-core/bowtie/build/meta.yml
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