From 8d47aa31bcefbe0b102f4343ab2a38414c8da47a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 20 Apr 2020 16:39:01 +0200
Subject: [PATCH] nf_modules: disable scratch for psmn
---
src/.update_config.sh | 2 ++
src/nf_modules/bedtools/fasta_from_bed.config | 1 -
src/nf_modules/bowtie/indexing.config | 1 -
src/nf_modules/bowtie/mapping_paired.config | 1 -
src/nf_modules/bowtie/mapping_single.config | 1 -
src/nf_modules/bowtie2/indexing.config | 1 -
src/nf_modules/bowtie2/mapping_paired.config | 1 -
src/nf_modules/bowtie2/mapping_single.config | 1 -
src/nf_modules/bwa/indexing.config | 1 -
src/nf_modules/bwa/mapping_paired.config | 1 -
src/nf_modules/cutadapt/adaptor_removal_paired.config | 1 -
src/nf_modules/cutadapt/adaptor_removal_single.config | 1 -
src/nf_modules/cutadapt/trimming_paired.config | 1 -
src/nf_modules/cutadapt/trimming_single.config | 1 -
src/nf_modules/deeptools/bam_to_bigwig.config | 1 -
src/nf_modules/deeptools/compute_matrix.config | 1 -
src/nf_modules/deeptools/plot_profile.config | 1 -
src/nf_modules/fastp/fastp_paired.config | 1 -
src/nf_modules/fastp/fastp_single.config | 1 -
src/nf_modules/fastqc/fastqc_paired.config | 1 -
src/nf_modules/fastqc/fastqc_single.config | 1 -
src/nf_modules/hisat2/indexing.config | 1 -
src/nf_modules/htseq/htseq.config | 1 -
src/nf_modules/kallisto/indexing.config | 1 -
src/nf_modules/kallisto/mapping_paired.config | 1 -
src/nf_modules/kallisto/mapping_single.config | 1 -
src/nf_modules/macs2/peak_calling.config | 1 -
src/nf_modules/multiqc/multiqc_paired.config | 1 -
src/nf_modules/multiqc/multiqc_single.config | 1 -
src/nf_modules/music/peak_calling_single.config | 1 -
src/nf_modules/rsem/indexing.config | 1 -
src/nf_modules/rsem/quantification_paired.config | 1 -
src/nf_modules/rsem/quantification_single.config | 1 -
src/nf_modules/sambamba/index_bams.config | 1 -
src/nf_modules/sambamba/sort_bams.config | 1 -
src/nf_modules/sambamba/split_bams.config | 1 -
src/nf_modules/samblaster/dedup_sams.config | 1 -
src/nf_modules/samtools/filter_bams.config | 1 -
src/nf_modules/samtools/index_bams.config | 1 -
src/nf_modules/samtools/sort_bams.config | 1 -
src/nf_modules/samtools/split_bams.config | 1 -
src/nf_modules/sratoolkit/fastqdump.config | 1 -
src/nf_modules/star/indexing.config | 1 -
src/nf_modules/star/mapping_paired.config | 1 -
src/nf_modules/star/mapping_single.config | 1 -
src/nf_modules/subread/subread.config | 1 -
src/nf_modules/urqt/trimming_paired.config | 1 -
src/nf_modules/urqt/trimming_single.config | 1 -
48 files changed, 2 insertions(+), 47 deletions(-)
diff --git a/src/.update_config.sh b/src/.update_config.sh
index e8f4fc9b..0beb2b1b 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -28,3 +28,5 @@ fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
# we update the psmn config to singularity
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 {}
+
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index a59f2573..6b642d67 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 10e15a38..56d24810 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 591528f9..7f564233 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 591528f9..7f564233 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 9c3fc8ec..5248f81c 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 140f6740..e3d7b7c6 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 140f6740..e3d7b7c6 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 03b85b1c..ba8af39e 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bwa:0.7.17"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 73da4757..94f3904d 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bwa:0.7.17"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 6def9752..8eb32108 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 6def9752..8eb32108 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index f813ab4f..0d27d53f 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index f813ab4f..0d27d53f 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 81fac55d..99461159 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index d020de9a..36279710 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: compute_matrix {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 5dec8218..627384e0 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: plot_profile {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 68f316c5..4545a988 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 68f316c5..4545a988 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 98e4c1df..fb8c8b2e 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 98e4c1df..fb8c8b2e 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index ba2915cb..074e5311 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/hisat2:2.1.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 72d14bec..354c2607 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/htseq:0.11.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index ef535de8..3b60bf84 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index d4bc1680..a74e8ea3 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index d4bc1680..a74e8ea3 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 2d250ef0..e272f038 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: peak_calling {
container = "lbmc/macs2:2.1.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 68d4b992..370a3e06 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -35,7 +35,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 7dbea6c6..6926341d 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 19d8002b..16df88bc 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -42,7 +42,6 @@ profiles {
process{
withName: compute_mappability {
container = "lbmc/music:6613c53"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 9a3d570c..004755f5 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 5371df44..3570af32 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 5371df44..3570af32 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 5e710fca..baa6c562 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 4a551993..17ed79c4 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 86934b58..3394ef09 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index c7f2dc36..bb2612c6 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: dedup_sam {
container = "lbmc/sambamba:0.6.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 17e7fefd..a5cce9de 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: filter_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 234119a0..fb362480 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index dd020ab0..c1ee3f37 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index cd34b085..6507405f 100644
--- 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"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index cc260862..e0708d7a 100644
--- 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"
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index 490aea02..d3d5edae 100644
--- 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"
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index e737ad12..2787b425 100644
--- 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"
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index e737ad12..2787b425 100644
--- 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"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 9ddbadb0..715e6136 100644
--- 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"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index a7dd1111..e740020e 100644
--- 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"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index a2719bd3..8df07c4e 100644
--- 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"
--
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