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

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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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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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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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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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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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8 changes: 4 additions & 4 deletions workflows/rnaseq.nf
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Expand Up @@ -92,14 +92,14 @@ 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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