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Reorganise local modules into subfolder/main.nf for consistency #1083

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merged 7 commits into from
Oct 11, 2023
Merged

Reorganise local modules into subfolder/main.nf for consistency #1083

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3112795
Reorganises local modules into subfolder/main.nf
adamrtalbot Oct 5, 2023
9a36b98
[automated] Fix linting with Prettier
nf-core-bot Oct 5, 2023
966e19c
Changes:
adamrtalbot Oct 5, 2023
308081f
CHANGELOG
adamrtalbot Oct 5, 2023
6191d72
Merge branch 'dev' into reorg_local_modules_to_subfolders
drpatelh Oct 11, 2023
ed219ad
Apply suggestions from code review
drpatelh Oct 11, 2023
41afa96
Update workflows/rnaseq.nf
drpatelh Oct 11, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +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 #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
- [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability

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0 modules/local/bedtools_genomecov.nf → modules/local/bedtools_genomecov/main.nf
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0 modules/local/cat_additional_fasta.nf → modules/local/cat_additional_fasta/main.nf
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0 modules/local/deseq2_qc.nf → modules/local/deseq2_qc/main.nf
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0 modules/local/dupradar.nf → modules/local/dupradar/main.nf
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0 modules/local/gtf2bed.nf → modules/local/gtf2bed/main.nf
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0 modules/local/gtf_gene_filter.nf → modules/local/gtf_gene_filter/main.nf
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0 modules/local/multiqc.nf → modules/local/multiqc/main.nf
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0 modules/local/multiqc_custom_biotype.nf → modules/local/multiqc_custom_biotype/main.nf
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0 ...l/preprocess_transcripts_fasta_gencode.nf → ...process_transcripts_fasta_gencode/main.nf
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0 modules/local/rsem_merge_counts.nf → modules/local/rsem_merge_counts/main.nf
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0 modules/local/salmon_summarizedexperiment.nf → ...local/salmon_summarizedexperiment/main.nf
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0 modules/local/salmon_tx2gene.nf → modules/local/salmon_tx2gene/main.nf
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0 modules/local/salmon_tximport.nf → modules/local/salmon_tximport/main.nf
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0 modules/local/star_align_igenomes.nf → modules/local/star_align_igenomes/main.nf
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0 ...les/local/star_genomegenerate_igenomes.nf → ...ocal/star_genomegenerate_igenomes/main.nf
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0 modules/local/umitools_prepareforrsem.nf → ...les/local/umitools_prepareforrsem/main.nf
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6 changes: 3 additions & 3 deletions subworkflows/local/align_star.nf → subworkflows/local/align_star/main.nf
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Expand Up @@ -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'
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:
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50 changes: 25 additions & 25 deletions subworkflows/local/prepare_genome.nf → subworkflows/local/prepare_genome/main.nf
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Expand Up @@ -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'
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'
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:
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6 changes: 3 additions & 3 deletions subworkflows/local/quantify_rsem.nf → subworkflows/local/quantify_rsem/main.nf
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Expand Up @@ -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'
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:
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16 changes: 8 additions & 8 deletions subworkflows/local/quantify_salmon.nf → subworkflows/local/quantify_salmon/main.nf
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Expand Up @@ -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'
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'
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:
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10 changes: 5 additions & 5 deletions workflows/rnaseq.nf
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Expand Up @@ -85,21 +85,21 @@ ch_biotypes_header_multiqc = file("$projectDir/assets/multiqc/biotypes_header.
//
// MODULE: Loaded from modules/local/
//
include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov'
include { BEDTOOLS_GENOMECOV } from '../modules/local/bedtools_genomecov/main'
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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 { 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'
include { ALIGN_STAR } from '../subworkflows/local/align_star'
include { QUANTIFY_RSEM } from '../subworkflows/local/quantify_rsem'
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'

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