remove copying for psmn config

src/.update_config.sh

@@ -29,4 +29,4 @@ fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
 fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n    singularity.enabled = true\n    singularity.cacheDir = "$baseDir/.singularity_psmn/"\n    singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
 fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
 fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*scratch = true(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
-
+fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*stageInMode = "copy"\n\s*stageOutMode = "rsync"(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}

src/nf_modules/bedtools/fasta_from_bed.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: fasta_from_bed {
         container = "lbmc/bedtools:2.25.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/bowtie/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/bowtie:1.2.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"

src/nf_modules/bowtie/mapping_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/bowtie:1.2.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bowtie/mapping_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/bowtie:1.2.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bowtie2/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/bowtie2:2.3.4.1"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bowtie2/mapping_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/bowtie2:2.3.4.1"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bowtie2/mapping_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/bowtie2:2.3.4.1"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bwa/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/bwa:0.7.17"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/bwa/mapping_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/bwa:0.7.17"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: adaptor_removal {
         container = "lbmc/cutadapt:2.4"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: adaptor_removal {
         container = "lbmc/cutadapt:2.4"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/trimming_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: trimming {
         container = "lbmc/cutadapt:2.4"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/trimming_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: trimming {
         container = "lbmc/cutadapt:2.4"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -34,8 +34,6 @@ profiles {
     process{
       withName: index_bam {
         container = "lbmc/deeptools:3.0.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/deeptools/compute_matrix.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: compute_matrix {
         container = "lbmc/deeptools:3.0.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/deeptools/plot_profile.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: plot_profile {
         container = "lbmc/deeptools:3.0.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/fastp/fastp_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: fastp_fastq {
         container = "lbmc/fastp:0.19.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/fastp/fastp_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: fastp_fastq {
         container = "lbmc/fastp:0.19.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/fastqc/fastqc_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: fastqc_fastq {
         container = "lbmc/fastqc:0.11.5"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1