Revert "Use config setting to set publish mode once"

This reverts commit eca3bd6.

conf/modules.config

@@ -10,17 +10,16 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow {
-    defaults {
-        publishDir = [
-            mode: params.publish_dir_mode,
-        ]
-    }
-}
+def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
+
+//
+// General configuration options
+//
 
 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 }
     ]
 }

subworkflows/local/align_star.nf

@@ -49,15 +49,18 @@ workflow ALIGN_STAR {
     align_publish_dir = [
         [
             path: "${params.outdir}/${params.aligner}/log",
+            mode: params.publish_dir_mode,
             pattern: '*.{out,tab}'
         ],
         [
             path: "${params.outdir}/${params.aligner}",
+            mode: params.publish_dir_mode,
             pattern: '*.bam',
             enabled: params.save_align_intermeds
         ],
         [
             path: "${params.outdir}/${params.aligner}/unmapped",
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz',
             enabled: params.save_unaligned
         ]
@@ -96,6 +99,7 @@ workflow ALIGN_STAR {
     sort_ext_prefix  = { "${meta.id}.sorted" }
     sort_publish_dir = [
         path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
         pattern: "*.bam",
         enabled: ( !params.with_umi && params.skip_markduplicates ) ||
             params.save_align_intermeds ||
@@ -104,6 +108,7 @@ workflow ALIGN_STAR {
     index_ext_args = params.bam_csi_index ? '-c' : ''
     index_publish_dir = [
         path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
         pattern: "*.{bai,csi}",
         enabled: ( !params.with_umi && params.skip_markduplicates ) ||
             params.save_align_intermeds ||
@@ -112,6 +117,7 @@ workflow ALIGN_STAR {
     stats_ext_prefix = { "${meta.id}.sorted.bam" }
     stats_publish_dir = [
         path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
         pattern: "*.{stats,flagstat,idxstats}"
     ]
     BAM_SORT_STATS_SAMTOOLS (

subworkflows/local/input_check.nf

@@ -11,6 +11,7 @@ workflow INPUT_CHECK {
     main:
     SAMPLESHEET_CHECK.config.publishDir = [
         path: "${params.outdir}/pipeline_info",
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
     SAMPLESHEET_CHECK ( samplesheet )

subworkflows/local/prepare_genome.nf

@@ -57,11 +57,13 @@ workflow PREPARE_GENOME {
 
     genome_publish_dir = [
         path: "${params.outdir}/genome",
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         enabled: params.save_reference
     ]
     genome_index_publish_dir = [
         path: "${params.outdir}/genome/index",
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         enabled: params.save_reference
     ]

subworkflows/local/quantify_rsem.nf

@@ -29,15 +29,18 @@ workflow QUANTIFY_RSEM {
     RSEM_CALCULATEEXPRESSION.config.publishDir = [
         [
             path: "${params.outdir}/${params.aligner}",
+            mode: params.publish_dir_mode,
             pattern: "*.{stat,results}"
         ],
         [
             path: "${params.outdir}/${params.aligner}",
+            mode: params.publish_dir_mode,
             pattern: "*.bam",
             enabled: params.save_align_intermeds
         ],
         [
             path: "${params.outdir}/${params.aligner}/log",
+            mode: params.publish_dir_mode,
             pattern: "*.log"
         ]
     ]
@@ -50,20 +53,23 @@ workflow QUANTIFY_RSEM {
     sort_ext_prefix = { "${meta.id}.sorted" }
     sort_publish_dir = [
         path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
         pattern: "*.bam",
         enabled: params.save_align_intermeds ||
             params.skip_markduplicates
     ]
     index_ext_args = params.bam_csi_index ? '-c' : ''
     index_publish_dir = [
         path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
         pattern: "*.{bai,csi}",
         enabled: params.save_align_intermeds ||
             params.skip_markduplicates
     ]
     stats_ext_prefix = { "${meta.id}.sorted.bam" }
     stats_publish_dir = [
         path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
         pattern: "*.{stats,flagstat,idxstats}"
     ]
     BAM_SORT_STATS_SAMTOOLS (
@@ -83,6 +89,7 @@ workflow QUANTIFY_RSEM {
     //
     RSEM_MERGE_COUNTS.config.publishDir = [
         path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
     RSEM_MERGE_COUNTS (

subworkflows/local/quantify_salmon.nf

@@ -27,6 +27,7 @@ workflow QUANTIFY_SALMON {
 
     publish_dir = [
         path: publish_dir_path,
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
@@ -36,6 +37,7 @@ workflow QUANTIFY_SALMON {
     SALMON_QUANT.config.ext.args = params.extra_salmon_quant_args ?: ''
     SALMON_QUANT.config.publishDir = [
         path: publish_dir_path,
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
     ]
     SALMON_QUANT ( reads, index, gtf, transcript_fasta, alignment_mode, lib_type )