nf_modules: disable scratch for psmn

8d47aa31 · Laurent Modolo · 670315f5 · 8d47aa31 · 8d47aa31 · 8d47aa31
Unverified Commit 8d47aa31 authored 4 years ago by Laurent Modolo
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: split_bam {
        container = "lbmc/samtools:1.7"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: fastq_dump {
        container = "lbmc/sratoolkit:2.8.2"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: index_fasta {
        container = "lbmc/star:2.7.3a"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: mapping_fastq {
        container = "lbmc/star:2.7.3a"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: mapping_fastq {
        container = "lbmc/star:2.7.3a"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -34,7 +34,6 @@ profiles {
    process{
      withName: sort_bam {
        container = "lbmc/subread:1.6.4"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: trimming {
        container = "lbmc/urqt:d62c1f8"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"

--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -26,7 +26,6 @@ profiles {
    process{
      withName: trimming {
        container = "lbmc/urqt:d62c1f8"
-        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"