From 9f0502eb81916362c3ad732e4b59d77be940f2ff Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Fri, 3 Aug 2018 10:58:02 +0200
Subject: [PATCH] changes to destination folders
---
src/RNAseq_sen1D_bowtie2_SE_CCA.nf | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/src/RNAseq_sen1D_bowtie2_SE_CCA.nf b/src/RNAseq_sen1D_bowtie2_SE_CCA.nf
index f16c1f3..e356ac6 100644
--- a/src/RNAseq_sen1D_bowtie2_SE_CCA.nf
+++ b/src/RNAseq_sen1D_bowtie2_SE_CCA.nf
@@ -22,7 +22,7 @@ fastq_files.into{fastq_files_adaptor; fastq_files_fastq}
process fastqc_fastq {
tag "$reads.baseName"
- publishDir "results/fastq_SE/fastqc/raw", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/fastqc/raw", mode: 'copy'
input:
file reads from fastq_files_fastq
@@ -57,7 +57,7 @@ fastq_files_cut.into{fastq_files_cut_randombp; fastq_files_cut_fastq}
process fastqc_fastq_cutadapt {
tag "$reads.baseName"
- publishDir "results/fastq_SE/fastqc/adaptor_removal/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/fastqc/adaptor_removal/", mode: 'copy'
input:
file (reads) from fastq_files_cut_fastq
@@ -73,7 +73,7 @@ fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
process random_bases_4_trimming {
tag "$reads.baseName"
- publishDir "results/fastq_SE/adaptor_removal/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/adaptor_removal/", mode: 'copy'
input:
file reads from fastq_files_cut_randombp
@@ -93,7 +93,7 @@ fastq_files_cut4.into{fastq_files_trim; fastq_files_cut4_fastq}
process fastqc_fastq_randombp {
tag "$reads.baseName"
- publishDir "results/fastq_SE/fastqc/random_bases_4_trimming/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/fastqc/random_bases_4_trimming/", mode: 'copy'
input:
file reads from fastq_files_cut4_fastq
@@ -121,7 +121,7 @@ fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
process trimming {
tag "${reads}"
cpus 4
- publishDir "results/fastq_SE/trimming/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/trimming/", mode: 'copy'
input:
file reads from fastq_files_trim
@@ -142,7 +142,7 @@ fastq_files_urqt.into{fastq_files_CCA; fastq_files_urqt_fastq}
process fastqc_fastq_urqt {
tag "$reads.baseName"
- publishDir "results/fastq_SE/fastqc/urqt/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/fastqc/urqt/", mode: 'copy'
input:
file reads from fastq_files_urqt_fastq
@@ -218,7 +218,7 @@ fi
process mapping_fastq {
tag "$reads.baseName"
cpus 4
- publishDir "results/mapping_SE/bams/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/mapping_SE_CCA/bams/", mode: 'copy'
input:
file reads from fastq_files_cut_CCA
@@ -270,7 +270,7 @@ samtools view -hb -q 2 ${bam} > ${bam}_filtered.bam
process multiqc {
tag "$repport"
- publishDir "results/fastq_SE/multiqc/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/fastq_SE_filtered/multiqc/CCA_removal", mode: 'copy'
cpus = 1
input:
@@ -292,7 +292,7 @@ multiqc -f .
process sort_bam {
tag "$bam.baseName"
cpus 4
- publishDir "results/mapping_SE/bams/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/mapping_SE_CCA/bams/", mode: 'copy'
input:
file bam from filtered_bam_files
@@ -308,7 +308,7 @@ samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
process index_bam {
tag "$bam.baseName"
- publishDir "results/mapping_SE/bams/", mode: 'copy'
+ publishDir "results/SE_CCA_sequencing/mapping_SE_CCA/bams/", mode: 'copy'
input:
file bam from sorted_bam_files
output:
--
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