nf_module: remove publishDir instruction

src/nf_modules/bedtools/main.nf

@@ -5,7 +5,6 @@ process fasta_from_bed {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bed.baseName}"
-  publishDir "results/fasta/", mode: 'copy'
 
   input:
   path fasta
@@ -25,7 +24,6 @@ process bam_to_fastq_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bam_id}"
-  publishDir "results/mapping/fastq/", mode: 'copy'
 
   input:
   tuple val(bam_id), path(bam)
@@ -44,7 +42,6 @@ process bam_to_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bam_id}"
-  publishDir "results/mapping/fastq/", mode: 'copy'
 
   input:
   tuple val(bam_id), path(bam)

src/nf_modules/bowtie/main.nf

@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -31,7 +30,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
@@ -69,7 +67,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index

src/nf_modules/bowtie2/main.nf

@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -32,7 +31,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
@@ -71,7 +69,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index

src/nf_modules/cutadapt/main.nf

@@ -10,7 +10,6 @@ process adaptor_removal_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -31,7 +30,6 @@ process adaptor_removal_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)
@@ -52,7 +50,6 @@ process trimming_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)

src/nf_modules/deeptools/main.nf

@@ -23,7 +23,6 @@ process bam_to_bigwig {
   label "big_mem_multi_cpus"
   tag "$file_id"
 
-  publishDir "results/mapping/bigwig/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam), path(idx)
@@ -42,7 +41,6 @@ process compute_matrix {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${bed_file_id}"
-  publishDir "results/metagene/region_matrix/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bw)
@@ -66,7 +64,6 @@ process plot_profile {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/metagene/region_matrix/", mode: 'copy'
 
   input:
     tuple val(file_id), path(matrix)

src/nf_modules/fastqc/main.nf

@@ -5,7 +5,6 @@ process fastqc_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -24,7 +23,6 @@ process fastqc_fastq_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)

src/nf_modules/kallisto/main.nf

@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -26,7 +25,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
   path index
@@ -50,7 +48,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
   path index

src/nf_modules/macs2/main.nf

@@ -5,7 +5,6 @@ process peak_calling {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${file_id}"
-  publishDir "results/peak_calling/${file_id}", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam_ip), path(bam_control)

src/nf_modules/multiqc/main.nf

@@ -5,7 +5,6 @@ process multiqc {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$report[0].baseName"
-  publishDir "results/QC/multiqc/", mode: 'copy'
 
   input:
     path report

src/nf_modules/picard/main.nf

@@ -5,7 +5,6 @@ process mark_duplicate {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/mapping/ddup/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam)

src/nf_modules/urqt/main.nf

@@ -7,7 +7,6 @@ process trimming_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${reads}"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -29,7 +28,6 @@ process trimming_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)