From ed7fec139bf6cd614b730fcd3e0cdf9807106548 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 3 Feb 2021 15:28:26 +0100
Subject: [PATCH] nf_module: remove publishDir instruction

---
 src/nf_modules/bedtools/main.nf  | 3 ---
 src/nf_modules/bowtie/main.nf    | 3 ---
 src/nf_modules/bowtie2/main.nf   | 3 ---
 src/nf_modules/cutadapt/main.nf  | 3 ---
 src/nf_modules/deeptools/main.nf | 3 ---
 src/nf_modules/fastqc/main.nf    | 2 --
 src/nf_modules/kallisto/main.nf  | 3 ---
 src/nf_modules/macs2/main.nf     | 1 -
 src/nf_modules/multiqc/main.nf   | 1 -
 src/nf_modules/picard/main.nf    | 1 -
 src/nf_modules/urqt/main.nf      | 2 --
 11 files changed, 25 deletions(-)

diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index bd4a1890..f0bef131 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/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)
diff --git a/src/nf_modules/bowtie/main.nf b/src/nf_modules/bowtie/main.nf
index d507b6b4..c95c47f0 100644
--- a/src/nf_modules/bowtie/main.nf
+++ b/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
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 22465bae..c852c31d 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/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
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index 0859ea92..020101fe 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/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)
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 3d012796..4a60dabe 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/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)
diff --git a/src/nf_modules/fastqc/main.nf b/src/nf_modules/fastqc/main.nf
index 4a209501..599101f6 100644
--- a/src/nf_modules/fastqc/main.nf
+++ b/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)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 0517a1b5..bb80e4b3 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/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
diff --git a/src/nf_modules/macs2/main.nf b/src/nf_modules/macs2/main.nf
index e30e0ee2..139a8db6 100644
--- a/src/nf_modules/macs2/main.nf
+++ b/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)
diff --git a/src/nf_modules/multiqc/main.nf b/src/nf_modules/multiqc/main.nf
index 1a3efda7..3b360f35 100644
--- a/src/nf_modules/multiqc/main.nf
+++ b/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
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 0faec2e0..a7326f3d 100644
--- a/src/nf_modules/picard/main.nf
+++ b/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)
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
index 48a1a3ec..6744856a 100644
--- a/src/nf_modules/urqt/main.nf
+++ b/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)
-- 
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