changes to destination folders

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: