From 311279532694ce7520164ce4d65a388c0cd11f60 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 5 Oct 2023 12:06:28 +0100 Subject: [PATCH 1/6] Reorganises local modules into subfolder/main.nf Changes: - Moves every local module into a named subfolder - Each module uses a main.nf file - Improves consistency between modules (local and nf-core) - Should make it easier to create nf-tests Fixes #1080 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir \u003cOUTDIR\u003e`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --- CHANGELOG.md | 3 ++- .../main.nf} | 0 .../main.nf} | 0 .../local/{deseq2_qc.nf => deseq2_qc/main.nf} | 0 modules/local/{dupradar.nf => dupradar/main.nf} | 0 modules/local/{gtf2bed.nf => gtf2bed/main.nf} | 0 .../main.nf} | 0 modules/local/{multiqc.nf => multiqc/main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 .../main.nf} | 0 subworkflows/local/align_star.nf | 2 +- subworkflows/local/prepare_genome.nf | 10 +++++----- subworkflows/local/quantify_rsem.nf | 2 +- subworkflows/local/quantify_salmon.nf | 12 ++++++------ workflows/rnaseq.nf | 16 ++++++++-------- 22 files changed, 23 insertions(+), 22 deletions(-) rename modules/local/{bedtools_genomecov.nf => bedtools_genomecov/main.nf} (100%) rename modules/local/{cat_additional_fasta.nf => cat_additional_fasta/main.nf} (100%) rename modules/local/{deseq2_qc.nf => deseq2_qc/main.nf} (100%) rename modules/local/{dupradar.nf => dupradar/main.nf} (100%) rename modules/local/{gtf2bed.nf => gtf2bed/main.nf} (100%) rename modules/local/{gtf_gene_filter.nf => gtf_gene_filter/main.nf} (100%) rename modules/local/{multiqc.nf => multiqc/main.nf} (100%) rename modules/local/{multiqc_custom_biotype.nf => multiqc_custom_biotype/main.nf} (100%) rename modules/local/{preprocess_transcripts_fasta_gencode.nf => preprocess_transcripts_fasta_gencode/main.nf} (100%) rename modules/local/{rsem_merge_counts.nf => rsem_merge_counts/main.nf} (100%) rename modules/local/{salmon_summarizedexperiment.nf => salmon_summarizedexperiment/main.nf} (100%) rename modules/local/{salmon_tx2gene.nf => salmon_tx2gene/main.nf} (100%) rename modules/local/{salmon_tximport.nf => salmon_tximport/main.nf} (100%) rename modules/local/{star_align_igenomes.nf => star_align_igenomes/main.nf} (100%) rename modules/local/{star_genomegenerate_igenomes.nf => star_genomegenerate_igenomes/main.nf} (100%) rename modules/local/{umitools_prepareforrsem.nf => umitools_prepareforrsem/main.nf} (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index c589534d3..0857884f9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module - +- [PR #XXX](https://github.com/nf-core/rnaseq/pull/xxx) - Move local modules to subfolder + ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02 ### Credits diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov/main.nf similarity index 100% rename from modules/local/bedtools_genomecov.nf rename to modules/local/bedtools_genomecov/main.nf diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta/main.nf similarity index 100% rename from modules/local/cat_additional_fasta.nf rename to modules/local/cat_additional_fasta/main.nf diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc/main.nf similarity index 100% rename from modules/local/deseq2_qc.nf rename to modules/local/deseq2_qc/main.nf diff --git a/modules/local/dupradar.nf b/modules/local/dupradar/main.nf similarity index 100% rename from modules/local/dupradar.nf rename to modules/local/dupradar/main.nf diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed/main.nf similarity index 100% rename from modules/local/gtf2bed.nf rename to modules/local/gtf2bed/main.nf diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter/main.nf similarity index 100% rename from modules/local/gtf_gene_filter.nf rename to modules/local/gtf_gene_filter/main.nf diff --git a/modules/local/multiqc.nf b/modules/local/multiqc/main.nf similarity index 100% rename from modules/local/multiqc.nf rename to modules/local/multiqc/main.nf diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype/main.nf similarity index 100% rename from modules/local/multiqc_custom_biotype.nf rename to modules/local/multiqc_custom_biotype/main.nf diff --git a/modules/local/preprocess_transcripts_fasta_gencode.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf similarity index 100% rename from modules/local/preprocess_transcripts_fasta_gencode.nf rename to modules/local/preprocess_transcripts_fasta_gencode/main.nf diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts/main.nf similarity index 100% rename from modules/local/rsem_merge_counts.nf rename to modules/local/rsem_merge_counts/main.nf diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment/main.nf similarity index 100% rename from modules/local/salmon_summarizedexperiment.nf rename to modules/local/salmon_summarizedexperiment/main.nf diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene/main.nf similarity index 100% rename from modules/local/salmon_tx2gene.nf rename to modules/local/salmon_tx2gene/main.nf diff --git a/modules/local/salmon_tximport.nf b/modules/local/salmon_tximport/main.nf similarity index 100% rename from modules/local/salmon_tximport.nf rename to modules/local/salmon_tximport/main.nf diff --git a/modules/local/star_align_igenomes.nf b/modules/local/star_align_igenomes/main.nf similarity index 100% rename from modules/local/star_align_igenomes.nf rename to modules/local/star_align_igenomes/main.nf diff --git a/modules/local/star_genomegenerate_igenomes.nf b/modules/local/star_genomegenerate_igenomes/main.nf similarity index 100% rename from modules/local/star_genomegenerate_igenomes.nf rename to modules/local/star_genomegenerate_igenomes/main.nf diff --git a/modules/local/umitools_prepareforrsem.nf b/modules/local/umitools_prepareforrsem/main.nf similarity index 100% rename from modules/local/umitools_prepareforrsem.nf rename to modules/local/umitools_prepareforrsem/main.nf diff --git a/subworkflows/local/align_star.nf b/subworkflows/local/align_star.nf index ffa027257..1ac3be9e2 100644 --- a/subworkflows/local/align_star.nf +++ b/subworkflows/local/align_star.nf @@ -3,7 +3,7 @@ // include { STAR_ALIGN } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN_IGENOMES } from '../../modules/local/star_align_igenomes' +include { STAR_ALIGN_IGENOMES } from '../../modules/local/star_align_igenomes/main' include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' workflow ALIGN_STAR { diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index b83126cd7..1d92505a1 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -25,11 +25,11 @@ include { SALMON_INDEX } from '../../modules/nf-core/salmon include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../modules/nf-core/rsem/preparereference/main' include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA } from '../../modules/nf-core/rsem/preparereference/main' -include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../modules/local/preprocess_transcripts_fasta_gencode' -include { GTF2BED } from '../../modules/local/gtf2bed' -include { CAT_ADDITIONAL_FASTA } from '../../modules/local/cat_additional_fasta' -include { GTF_GENE_FILTER } from '../../modules/local/gtf_gene_filter' -include { STAR_GENOMEGENERATE_IGENOMES } from '../../modules/local/star_genomegenerate_igenomes' +include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../modules/local/preprocess_transcripts_fasta_gencode/main' +include { GTF2BED } from '../../modules/local/gtf2bed/main' +include { CAT_ADDITIONAL_FASTA } from '../../modules/local/cat_additional_fasta/main' +include { GTF_GENE_FILTER } from '../../modules/local/gtf_gene_filter/main' +include { STAR_GENOMEGENERATE_IGENOMES } from '../../modules/local/star_genomegenerate_igenomes/main' workflow PREPARE_GENOME { take: diff --git a/subworkflows/local/quantify_rsem.nf b/subworkflows/local/quantify_rsem.nf index 666af33b1..fa81db065 100644 --- a/subworkflows/local/quantify_rsem.nf +++ b/subworkflows/local/quantify_rsem.nf @@ -3,7 +3,7 @@ // include { RSEM_CALCULATEEXPRESSION } from '../../modules/nf-core/rsem/calculateexpression/main' -include { RSEM_MERGE_COUNTS } from '../../modules/local/rsem_merge_counts' +include { RSEM_MERGE_COUNTS } from '../../modules/local/rsem_merge_counts/main' include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' workflow QUANTIFY_RSEM { diff --git a/subworkflows/local/quantify_salmon.nf b/subworkflows/local/quantify_salmon.nf index 4ab996b2c..1326c2a06 100644 --- a/subworkflows/local/quantify_salmon.nf +++ b/subworkflows/local/quantify_salmon.nf @@ -3,13 +3,13 @@ // include { SALMON_QUANT } from '../../modules/nf-core/salmon/quant/main' -include { SALMON_TX2GENE } from '../../modules/local/salmon_tx2gene' -include { SALMON_TXIMPORT } from '../../modules/local/salmon_tximport' +include { SALMON_TX2GENE } from '../../modules/local/salmon_tx2gene/main' +include { SALMON_TXIMPORT } from '../../modules/local/salmon_tximport/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../modules/local/salmon_summarizedexperiment' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../modules/local/salmon_summarizedexperiment' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../modules/local/salmon_summarizedexperiment' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../modules/local/salmon_summarizedexperiment' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../modules/local/salmon_summarizedexperiment/main' workflow QUANTIFY_SALMON { take: diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 72b7619a4..c6f16dabe 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -85,14 +85,14 @@ ch_biotypes_header_multiqc = file("$projectDir/assets/multiqc/biotypes_header. // // MODULE: Loaded from modules/local/ // -include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov' -include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc' -include { DESEQ2_QC as DESEQ2_QC_RSEM } from '../modules/local/deseq2_qc' -include { DESEQ2_QC as DESEQ2_QC_SALMON } from '../modules/local/deseq2_qc' -include { DUPRADAR } from '../modules/local/dupradar' -include { MULTIQC } from '../modules/local/multiqc' -include { MULTIQC_CUSTOM_BIOTYPE } from '../modules/local/multiqc_custom_biotype' -include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem.nf' +include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov/main' +include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc/main' +include { DESEQ2_QC as DESEQ2_QC_RSEM } from '../modules/local/deseq2_qc/main' +include { DESEQ2_QC as DESEQ2_QC_SALMON } from '../modules/local/deseq2_qc/main' +include { DUPRADAR } from '../modules/local/dupradar/main' +include { MULTIQC } from '../modules/local/multiqc/main' +include { MULTIQC_CUSTOM_BIOTYPE } from '../modules/local/multiqc_custom_biotype/main' +include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem/main' // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules From 9a36b98cf45e9e5d3f34d75874a8bbd99345b2f0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 5 Oct 2023 11:08:39 +0000 Subject: [PATCH 2/6] [automated] Fix linting with Prettier --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0857884f9..e11f7119d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,8 +23,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module -- [PR #XXX](https://github.com/nf-core/rnaseq/pull/xxx) - Move local modules to subfolder - +- [PR #XXX](https://github.com/nf-core/rnaseq/pull/xxx) - Move local modules to subfolder + ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02 ### Credits From 966e19cbb7dfd9c2568949b447486dc30007384a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 5 Oct 2023 12:23:45 +0100 Subject: [PATCH 3/6] Changes: - Moves every local subworkflow into a named subfolder - Each workflow uses a main.nf file - Improves consistency between subworkflows (local and nf-core) - Should make it easier to create nf-tests --- .../{align_star.nf => align_star/main.nf} | 6 +-- .../main.nf} | 50 +++++++++---------- .../main.nf} | 6 +-- .../main.nf} | 16 +++--- workflows/rnaseq.nf | 10 ++-- 5 files changed, 44 insertions(+), 44 deletions(-) rename subworkflows/local/{align_star.nf => align_star/main.nf} (93%) rename subworkflows/local/{prepare_genome.nf => prepare_genome/main.nf} (82%) rename subworkflows/local/{quantify_rsem.nf => quantify_rsem/main.nf} (91%) rename subworkflows/local/{quantify_salmon.nf => quantify_salmon/main.nf} (87%) diff --git a/subworkflows/local/align_star.nf b/subworkflows/local/align_star/main.nf similarity index 93% rename from subworkflows/local/align_star.nf rename to subworkflows/local/align_star/main.nf index 1ac3be9e2..28b1d612e 100644 --- a/subworkflows/local/align_star.nf +++ b/subworkflows/local/align_star/main.nf @@ -2,9 +2,9 @@ // Alignment with STAR // -include { STAR_ALIGN } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN_IGENOMES } from '../../modules/local/star_align_igenomes/main' -include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' +include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main' +include { STAR_ALIGN_IGENOMES } from '../../../modules/local/star_align_igenomes/main' +include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main' workflow ALIGN_STAR { take: diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome/main.nf similarity index 82% rename from subworkflows/local/prepare_genome.nf rename to subworkflows/local/prepare_genome/main.nf index 1d92505a1..41fcb6cff 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -2,34 +2,34 @@ // Uncompress and prepare reference genome files // -include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GFF } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip/main' -include { UNTAR as UNTAR_BBSPLIT_INDEX } from '../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_RSEM_INDEX } from '../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_HISAT2_INDEX } from '../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_SALMON_INDEX } from '../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_BBSPLIT_INDEX } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_RSEM_INDEX } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_HISAT2_INDEX } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_SALMON_INDEX } from '../../../modules/nf-core/untar/main' -include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main' -include { GFFREAD } from '../../modules/nf-core/gffread/main' -include { BBMAP_BBSPLIT } from '../../modules/nf-core/bbmap/bbsplit/main' -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate/main' -include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites/main' -include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build/main' -include { SALMON_INDEX } from '../../modules/nf-core/salmon/index/main' -include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../modules/nf-core/rsem/preparereference/main' -include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA } from '../../modules/nf-core/rsem/preparereference/main' +include { CUSTOM_GETCHROMSIZES } from '../../../modules/nf-core/custom/getchromsizes/main' +include { GFFREAD } from '../../../modules/nf-core/gffread/main' +include { BBMAP_BBSPLIT } from '../../../modules/nf-core/bbmap/bbsplit/main' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' +include { HISAT2_EXTRACTSPLICESITES } from '../../../modules/nf-core/hisat2/extractsplicesites/main' +include { HISAT2_BUILD } from '../../../modules/nf-core/hisat2/build/main' +include { SALMON_INDEX } from '../../../modules/nf-core/salmon/index/main' +include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference/main' +include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA } from '../../../modules/nf-core/rsem/preparereference/main' -include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../modules/local/preprocess_transcripts_fasta_gencode/main' -include { GTF2BED } from '../../modules/local/gtf2bed/main' -include { CAT_ADDITIONAL_FASTA } from '../../modules/local/cat_additional_fasta/main' -include { GTF_GENE_FILTER } from '../../modules/local/gtf_gene_filter/main' -include { STAR_GENOMEGENERATE_IGENOMES } from '../../modules/local/star_genomegenerate_igenomes/main' +include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode/main' +include { GTF2BED } from '../../../modules/local/gtf2bed/main' +include { CAT_ADDITIONAL_FASTA } from '../../../modules/local/cat_additional_fasta/main' +include { GTF_GENE_FILTER } from '../../../modules/local/gtf_gene_filter/main' +include { STAR_GENOMEGENERATE_IGENOMES } from '../../../modules/local/star_genomegenerate_igenomes/main' workflow PREPARE_GENOME { take: diff --git a/subworkflows/local/quantify_rsem.nf b/subworkflows/local/quantify_rsem/main.nf similarity index 91% rename from subworkflows/local/quantify_rsem.nf rename to subworkflows/local/quantify_rsem/main.nf index fa81db065..92305d67a 100644 --- a/subworkflows/local/quantify_rsem.nf +++ b/subworkflows/local/quantify_rsem/main.nf @@ -2,9 +2,9 @@ // Gene/transcript quantification with RSEM // -include { RSEM_CALCULATEEXPRESSION } from '../../modules/nf-core/rsem/calculateexpression/main' -include { RSEM_MERGE_COUNTS } from '../../modules/local/rsem_merge_counts/main' -include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' +include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression/main' +include { RSEM_MERGE_COUNTS } from '../../../modules/local/rsem_merge_counts/main' +include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main' workflow QUANTIFY_RSEM { take: diff --git a/subworkflows/local/quantify_salmon.nf b/subworkflows/local/quantify_salmon/main.nf similarity index 87% rename from subworkflows/local/quantify_salmon.nf rename to subworkflows/local/quantify_salmon/main.nf index 1326c2a06..1c69c56cb 100644 --- a/subworkflows/local/quantify_salmon.nf +++ b/subworkflows/local/quantify_salmon/main.nf @@ -2,14 +2,14 @@ // Pseudo-alignment and quantification with Salmon // -include { SALMON_QUANT } from '../../modules/nf-core/salmon/quant/main' -include { SALMON_TX2GENE } from '../../modules/local/salmon_tx2gene/main' -include { SALMON_TXIMPORT } from '../../modules/local/salmon_tximport/main' - -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_QUANT } from '../../../modules/nf-core/salmon/quant/main' +include { SALMON_TX2GENE } from '../../../modules/local/salmon_tx2gene/main' +include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport/main' + +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../../modules/local/salmon_summarizedexperiment/main' workflow QUANTIFY_SALMON { take: diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index c6f16dabe..3489bca77 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -97,11 +97,11 @@ include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../module // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' -include { ALIGN_STAR } from '../subworkflows/local/align_star' -include { QUANTIFY_RSEM } from '../subworkflows/local/quantify_rsem' -include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon' -include { QUANTIFY_SALMON as QUANTIFY_SALMON } from '../subworkflows/local/quantify_salmon' +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome/main' +include { ALIGN_STAR } from '../subworkflows/local/align_star/main' +include { QUANTIFY_RSEM } from '../subworkflows/local/quantify_rsem/main' +include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon/main' +include { QUANTIFY_SALMON as QUANTIFY_SALMON } from '../subworkflows/local/quantify_salmon/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 308081f4a95c33654058d07cca73912b0b6938f3 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 5 Oct 2023 12:28:50 +0100 Subject: [PATCH 4/6] CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e11f7119d..cf0d4ae0a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module -- [PR #XXX](https://github.com/nf-core/rnaseq/pull/xxx) - Move local modules to subfolder +- [PR #1083](https://github.com/nf-core/rnaseq/pull/1084) - Move local modules and subworkflows to subfolders ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02 From ed219ad8a6e90bd82933c8372158014f41f26883 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 21:25:54 +0200 Subject: [PATCH 5/6] Apply suggestions from code review --- subworkflows/local/align_star/main.nf | 6 +-- subworkflows/local/prepare_genome/main.nf | 50 +++++++++++----------- subworkflows/local/quantify_rsem/main.nf | 6 +-- subworkflows/local/quantify_salmon/main.nf | 16 +++---- workflows/rnaseq.nf | 24 +++++------ 5 files changed, 51 insertions(+), 51 deletions(-) diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf index 28b1d612e..479ed2379 100644 --- a/subworkflows/local/align_star/main.nf +++ b/subworkflows/local/align_star/main.nf @@ -2,9 +2,9 @@ // Alignment with STAR // -include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main' -include { STAR_ALIGN_IGENOMES } from '../../../modules/local/star_align_igenomes/main' -include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main' +include { STAR_ALIGN } from '../../../modules/nf-core/star/align' +include { STAR_ALIGN_IGENOMES } from '../../../modules/local/star_align_igenomes' +include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools' workflow ALIGN_STAR { take: diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 41fcb6cff..200957cda 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -2,34 +2,34 @@ // Uncompress and prepare reference genome files // -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip' +include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip' +include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip' +include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip' +include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip' -include { UNTAR as UNTAR_BBSPLIT_INDEX } from '../../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_RSEM_INDEX } from '../../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_HISAT2_INDEX } from '../../../modules/nf-core/untar/main' -include { UNTAR as UNTAR_SALMON_INDEX } from '../../../modules/nf-core/untar/main' +include { UNTAR as UNTAR_BBSPLIT_INDEX } from '../../../modules/nf-core/untar' +include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar' +include { UNTAR as UNTAR_RSEM_INDEX } from '../../../modules/nf-core/untar' +include { UNTAR as UNTAR_HISAT2_INDEX } from '../../../modules/nf-core/untar' +include { UNTAR as UNTAR_SALMON_INDEX } from '../../../modules/nf-core/untar' -include { CUSTOM_GETCHROMSIZES } from '../../../modules/nf-core/custom/getchromsizes/main' -include { GFFREAD } from '../../../modules/nf-core/gffread/main' -include { BBMAP_BBSPLIT } from '../../../modules/nf-core/bbmap/bbsplit/main' -include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { HISAT2_EXTRACTSPLICESITES } from '../../../modules/nf-core/hisat2/extractsplicesites/main' -include { HISAT2_BUILD } from '../../../modules/nf-core/hisat2/build/main' -include { SALMON_INDEX } from '../../../modules/nf-core/salmon/index/main' -include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference/main' -include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA } from '../../../modules/nf-core/rsem/preparereference/main' +include { CUSTOM_GETCHROMSIZES } from '../../../modules/nf-core/custom/getchromsizes' +include { GFFREAD } from '../../../modules/nf-core/gffread' +include { BBMAP_BBSPLIT } from '../../../modules/nf-core/bbmap/bbsplit' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate' +include { HISAT2_EXTRACTSPLICESITES } from '../../../modules/nf-core/hisat2/extractsplicesites' +include { HISAT2_BUILD } from '../../../modules/nf-core/hisat2/build' +include { SALMON_INDEX } from '../../../modules/nf-core/salmon/index' +include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference' +include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA } from '../../../modules/nf-core/rsem/preparereference' -include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode/main' -include { GTF2BED } from '../../../modules/local/gtf2bed/main' -include { CAT_ADDITIONAL_FASTA } from '../../../modules/local/cat_additional_fasta/main' -include { GTF_GENE_FILTER } from '../../../modules/local/gtf_gene_filter/main' -include { STAR_GENOMEGENERATE_IGENOMES } from '../../../modules/local/star_genomegenerate_igenomes/main' +include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode' +include { GTF2BED } from '../../../modules/local/gtf2bed' +include { CAT_ADDITIONAL_FASTA } from '../../../modules/local/cat_additional_fasta' +include { GTF_GENE_FILTER } from '../../../modules/local/gtf_gene_filter' +include { STAR_GENOMEGENERATE_IGENOMES } from '../../../modules/local/star_genomegenerate_igenomes' workflow PREPARE_GENOME { take: diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf index 92305d67a..4b7473634 100644 --- a/subworkflows/local/quantify_rsem/main.nf +++ b/subworkflows/local/quantify_rsem/main.nf @@ -2,9 +2,9 @@ // Gene/transcript quantification with RSEM // -include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression/main' -include { RSEM_MERGE_COUNTS } from '../../../modules/local/rsem_merge_counts/main' -include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main' +include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression' +include { RSEM_MERGE_COUNTS } from '../../../modules/local/rsem_merge_counts' +include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools' workflow QUANTIFY_RSEM { take: diff --git a/subworkflows/local/quantify_salmon/main.nf b/subworkflows/local/quantify_salmon/main.nf index 1c69c56cb..1b936d6fe 100644 --- a/subworkflows/local/quantify_salmon/main.nf +++ b/subworkflows/local/quantify_salmon/main.nf @@ -2,14 +2,14 @@ // Pseudo-alignment and quantification with Salmon // -include { SALMON_QUANT } from '../../../modules/nf-core/salmon/quant/main' -include { SALMON_TX2GENE } from '../../../modules/local/salmon_tx2gene/main' -include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport/main' - -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../../modules/local/salmon_summarizedexperiment/main' -include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../../modules/local/salmon_summarizedexperiment/main' +include { SALMON_QUANT } from '../../../modules/nf-core/salmon/quant' +include { SALMON_TX2GENE } from '../../../modules/local/salmon_tx2gene' +include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport' + +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE } from '../../../modules/local/salmon_summarizedexperiment' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED } from '../../../modules/local/salmon_summarizedexperiment' +include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT } from '../../../modules/local/salmon_summarizedexperiment' workflow QUANTIFY_SALMON { take: diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 3489bca77..f5213576a 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -86,22 +86,22 @@ ch_biotypes_header_multiqc = file("$projectDir/assets/multiqc/biotypes_header. // MODULE: Loaded from modules/local/ // include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov/main' -include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc/main' -include { DESEQ2_QC as DESEQ2_QC_RSEM } from '../modules/local/deseq2_qc/main' -include { DESEQ2_QC as DESEQ2_QC_SALMON } from '../modules/local/deseq2_qc/main' -include { DUPRADAR } from '../modules/local/dupradar/main' -include { MULTIQC } from '../modules/local/multiqc/main' -include { MULTIQC_CUSTOM_BIOTYPE } from '../modules/local/multiqc_custom_biotype/main' -include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem/main' +include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc' +include { DESEQ2_QC as DESEQ2_QC_RSEM } from '../modules/local/deseq2_qc' +include { DESEQ2_QC as DESEQ2_QC_SALMON } from '../modules/local/deseq2_qc' +include { DUPRADAR } from '../modules/local/dupradar' +include { MULTIQC } from '../modules/local/multiqc' +include { MULTIQC_CUSTOM_BIOTYPE } from '../modules/local/multiqc_custom_biotype' +include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem' // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome/main' -include { ALIGN_STAR } from '../subworkflows/local/align_star/main' -include { QUANTIFY_RSEM } from '../subworkflows/local/quantify_rsem/main' -include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon/main' -include { QUANTIFY_SALMON as QUANTIFY_SALMON } from '../subworkflows/local/quantify_salmon/main' +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' +include { ALIGN_STAR } from '../subworkflows/local/align_star' +include { QUANTIFY_RSEM } from '../subworkflows/local/quantify_rsem' +include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon' +include { QUANTIFY_SALMON as QUANTIFY_SALMON } from '../subworkflows/local/quantify_salmon' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 41afa96cc9845146933bb6a8c19556241cb0c77e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 21:26:43 +0200 Subject: [PATCH 6/6] Update workflows/rnaseq.nf --- workflows/rnaseq.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index f5213576a..4c281c865 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -85,7 +85,7 @@ ch_biotypes_header_multiqc = file("$projectDir/assets/multiqc/biotypes_header. // // MODULE: Loaded from modules/local/ // -include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov/main' +include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov' include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc' include { DESEQ2_QC as DESEQ2_QC_RSEM } from '../modules/local/deseq2_qc' include { DESEQ2_QC as DESEQ2_QC_SALMON } from '../modules/local/deseq2_qc'