remove copying for psmn config

src/nf_modules/fastqc/fastqc_single.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

src/nf_modules/hisat2/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/hisat2:2.1.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"

src/nf_modules/htseq/htseq.config

@@ -34,8 +34,6 @@ profiles {
     process{
       withName: sort_bam {
         container = "lbmc/htseq:0.11.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/kallisto/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/kallisto:0.44.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/kallisto/mapping_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/kallisto:0.44.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/kallisto/mapping_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/kallisto:0.44.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/macs2/peak_calling.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: peak_calling {
         container = "lbmc/macs2:2.1.2"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/multiqc/multiqc_paired.config

@@ -35,8 +35,6 @@ profiles {
     process{
       withName: fastqc_fastq {
         container = "lbmc/multiqc:1.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/multiqc/multiqc_single.config

@@ -34,8 +34,6 @@ profiles {
     process{
       withName: fastqc_fastq {
         container = "lbmc/multiqc:1.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/music/peak_calling_single.config

@@ -42,8 +42,6 @@ profiles {
     process{
       withName: compute_mappability {
         container = "lbmc/music:6613c53"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/rsem/indexing.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_fasta {
         container = "lbmc/rsem:1.3.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/rsem/quantification_paired.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/rsem:1.3.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/rsem/quantification_single.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: mapping_fastq {
         container = "lbmc/rsem:1.3.0"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/sambamba/index_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_bam {
         container = "lbmc/sambamba:0.6.9"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/sambamba/sort_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: sort_bam {
         container = "lbmc/sambamba:0.6.9"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4

src/nf_modules/sambamba/split_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: split_bam {
         container = "lbmc/sambamba:0.6.9"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/samblaster/dedup_sams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: dedup_sam {
         container = "lbmc/sambamba:0.6.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/samtools/filter_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: filter_bam {
         container = "lbmc/samtools:1.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/samtools/index_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: index_bam {
         container = "lbmc/samtools:1.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/samtools/sort_bams.config

@@ -26,8 +26,6 @@ profiles {
     process{
       withName: sort_bam {
         container = "lbmc/samtools:1.7"
-        stageInMode = "copy"
-        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32