Add output definition

Signed-off-by: Ben Sherman <[email protected]>

main.nf

@@ -164,6 +164,66 @@ workflow {
  )
 }
 
+output {
+ path(params.outdir) {
+ path('genome', enabled: params.save_reference) {
+ select 'GUNZIP_.*'
+ select 'MAKE_TRANSCRIPTS_FASTA'
+ select 'GFFREAD'
+ select 'GTF2BED'
+ select 'CAT_ADDITIONAL_FASTA'
+ select 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE'
+ select 'GTF_FILTER'
+ select 'CUSTOM_GETCHROMSIZES'
+ }
+
+ path('genome/index', enabled: params.save_reference) {
+ select 'UNTAR_.*'
+ select 'STAR_GENOMEGENERATE'
+ select 'STAR_GENOMEGENERATE_IGENOMES'
+ select 'HISAT2_BUILD'
+ select 'HISAT2_EXTRACTSPLICESITES'
+ select 'SALMON_INDEX'
+ select 'KALLISTO_INDEX'
+ select 'RSEM_PREPAREREFERENCE_GENOME'
+ select 'PREPARE_GENOME:BBMAP_BBSPLIT'
+ }
+
+ path(params.aligner) {
+ select '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT'
+ select '.*:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE'
+ select '.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT'
+ select '.*:QUANTIFY_STAR_SALMON:SE_.*'
+
+ path('umitools') {
+ select '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP', pattern: '*.tsv'
+ }
+
+ path('samtools_stats') {
+ select '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*', pattern: '*.{stats,flagstat,idxstats}'
+ select 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*', pattern: '*.{stats,flagstat,idxstats}'
+ }
+ }
+
+ path(params.aligner, enabled: params.save_align_intermeds || params.save_umi_intermeds) {
+ select 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT', pattern: '*.bam'
+ select 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON', pattern: '*.bam'
+ path('umitools/log') {
+ select 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON', pattern: '*.log'
+ }
+
+ select 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT', pattern: '*.bam'
+ select 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX', pattern: '*.bai'
+ path('samtools_stats') {
+ select 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*', pattern: '*.{stats,flagstat,idxstats}'
+ }
+
+ select '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP', pattern: '*.bam'
+ select '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX', pattern: '*.bai'
+ }
+ }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  THE END

nextflow.config

@@ -135,15 +135,6 @@ params {
 
 }
 
-// Default publishing logic for pipeline
-process {
- publishDir = [
- path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
-}
-
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 

subworkflows/local/prepare_genome/nextflow.config

@@ -1,114 +1,36 @@
 process {
- withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
  withName: 'UNTAR_.*' {
  ext.args2 = '--no-same-owner'
  }
 
- withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
  withName: 'GFFREAD' {
  ext.args = '--keep-exon-attrs -F -T'
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
- withName: 'HISAT2_EXTRACTSPLICESITES' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
 
  withName: 'SALMON_INDEX' {
  ext.args = { [
  params.gencode ? '--gencode' : '',
  params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
  ].join(' ').trim() }
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
 
  withName: 'KALLISTO_INDEX' {
  ext.args = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
 
  withName: 'RSEM_PREPAREREFERENCE_GENOME' {
  ext.args = '--star'
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
- withName: 'GTF2BED' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
- withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
 
  withName: 'GTF_FILTER' {
  ext.args = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
- }
-
- withName: 'CUSTOM_GETCHROMSIZES' {
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
 }
 
 if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
  process {
  withName: 'PREPARE_GENOME:BBMAP_BBSPLIT' {
  ext.args = 'build=1'
- publishDir = [
- path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
- mode: params.publish_dir_mode,
- saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
- ]
  }
  }
 }

workflows/rnaseq/nextflow.config

@@ -26,37 +26,12 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
  process {
  withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
  ext.args = { params.extra_salmon_quant_args ?: '' }
- publishDir = [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
- ]
  }
-
- withName: '.*:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE' {
- publishDir = [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
- }
-
  withName: '.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT' {
  ext.prefix = { "${quant_type}.merged" }
- publishDir = [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
  }
-
  withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
  ext.prefix = { "${params.pseudo_aligner}.merged" }
- publishDir = [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
- ]
  }
  withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE' {
  ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
@@ -77,58 +52,18 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
  withName: 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT' {
  ext.args = '-n'
  ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
- publishDir = [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
  }
 
  withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
  ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
- publishDir = [
- [
- path: { "${params.outdir}/${params.aligner}/umitools/log" },
- mode: params.publish_dir_mode,
- pattern: '*.log'
- ],
- [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
- ]
  }
 
  withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
  ext.prefix = { "${meta.id}.transcriptome.sorted" }
- publishDir = [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
- }
-
- withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
- publishDir = [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bai',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
  }
 
  withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
  ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
- publishDir = [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.{stats,flagstat,idxstats}',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
  }
 
  withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
@@ -138,37 +73,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
  params.umitools_umi_separator ? "--umi-separator='${params.umitools_umi_separator}'" : ''
  ].join(' ').trim() }
  ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
- publishDir = [
- [
- path: { "${params.outdir}/${params.aligner}/umitools" },
- mode: params.publish_dir_mode,
- pattern: '*.tsv'
- ],
- [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
- ]
- }
-
- withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
- publishDir = [
- path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bai',
- saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
- ]
  }
 
  withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
  ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
- publishDir = [
- path: { "${params.outdir}/${params.aligner}/samtools_stats" },
- mode: params.publish_dir_mode,
- pattern: '*.{stats,flagstat,idxstats}'
- ]
  }
  }
  }
@@ -182,11 +90,6 @@ if (!params.skip_alignment) {
  process {
  withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
  ext.prefix = { "${meta.id}.sorted.bam" }
- publishDir = [
- path: { "${params.outdir}/${params.aligner}/samtools_stats" },
- mode: params.publish_dir_mode,
- pattern: "*.{stats,flagstat,idxstats}"
- ]
  }
 
  withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
@@ -282,8 +185,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
  ext.prefix = { "${meta.id}.forward" }
  publishDir = [
  path: { "${params.outdir}/${params.aligner}/bigwig" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
  ]
  }
 
@@ -298,8 +199,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
  ext.prefix = { "${meta.id}.reverse" }
  publishDir = [
  path: { "${params.outdir}/${params.aligner}/bigwig" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
  ]
  }
  }
@@ -360,26 +259,20 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
  withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE' {
  publishDir = [
  path: { "${params.outdir}/${params.pseudo_aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
  ]
  }
 
  withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT' {
  ext.prefix = { "${quant_type}.merged" }
  publishDir = [
  path: { "${params.outdir}/${params.pseudo_aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
  ]
  }
 
  withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
  ext.args = '--assay_names counts,abundance'
  publishDir = [
  path: { "${params.outdir}/${params.pseudo_aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
  ]
  }
  withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE' {