Add complete output definition

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

main.nf

@@ -164,66 +164,6 @@ 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

modules/local/bedtools_genomecov/nextflow.config

@@ -3,9 +3,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
  process {
  withName: 'BEDTOOLS_GENOMECOV' {
  ext.args = '-split -du'
- publishDir = [
- enabled: false
- ]
  }
  }
 }

subworkflows/local/align_star/nextflow.config

@@ -15,25 +15,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
  params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
  params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
  ].flatten().unique(false).join(' ').trim() }
- publishDir = [
- [
- path: { "${params.outdir}/${params.aligner}/log" },
- mode: params.publish_dir_mode,
- pattern: '*.{out,tab}'
- ],
- [
- path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds ? it : null }
- ],
- [
- path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.fastq.gz',
- saveAs: { params.save_unaligned ? it : null }
- ]
- ]
  }
  }
 }

subworkflows/local/prepare_genome/main.nf

@@ -343,3 +343,33 @@ workflow PREPARE_GENOME {
  kallisto_index = ch_kallisto_index // channel: [ meta, path(kallisto/index/) ]
  versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
+
+output {
+ if( !params.save_reference )
+ return
+
+ path(params.outdir, mode: params.publish_dir_mode) {
+ path('genome') {
+ 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') {
+ 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'
+ }
+ }
+}

subworkflows/local/quantify_rsem/nextflow.config

@@ -8,32 +8,6 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
  '--estimate-rspd',
  '--seed 1'
  ].join(' ').trim()
- publishDir = [
- [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- pattern: "*.{stat,results}"
- ],
- [
- path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: "*.bam",
- saveAs: { params.save_align_intermeds ? it : null }
- ],
- [
- path: { "${params.outdir}/${params.aligner}/log" },
- mode: params.publish_dir_mode,
- pattern: "*.log"
- ]
- ]
- }
-
- withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
- publishDir = [
- path: { "${params.outdir}/${params.aligner}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
  }
  }
 }