From 87c79ae224afb834ffc01ec1668d0b71e1c4125b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 27 Apr 2020 15:48:29 +0200
Subject: [PATCH] remove copying for psmn config
---
src/.update_config.sh | 2 +-
src/nf_modules/bedtools/fasta_from_bed.config | 2 --
src/nf_modules/bowtie/indexing.config | 2 --
src/nf_modules/bowtie/mapping_paired.config | 2 --
src/nf_modules/bowtie/mapping_single.config | 2 --
src/nf_modules/bowtie2/indexing.config | 2 --
src/nf_modules/bowtie2/mapping_paired.config | 2 --
src/nf_modules/bowtie2/mapping_single.config | 2 --
src/nf_modules/bwa/indexing.config | 2 --
src/nf_modules/bwa/mapping_paired.config | 2 --
.../cutadapt/adaptor_removal_paired.config | 2 --
.../cutadapt/adaptor_removal_single.config | 2 --
src/nf_modules/cutadapt/trimming_paired.config | 2 --
src/nf_modules/cutadapt/trimming_single.config | 2 --
src/nf_modules/deeptools/bam_to_bigwig.config | 2 --
src/nf_modules/deeptools/compute_matrix.config | 2 --
src/nf_modules/deeptools/plot_profile.config | 2 --
src/nf_modules/fastp/fastp_paired.config | 2 --
src/nf_modules/fastp/fastp_single.config | 2 --
src/nf_modules/fastqc/fastqc_paired.config | 2 --
src/nf_modules/fastqc/fastqc_single.config | 2 --
src/nf_modules/hisat2/indexing.config | 2 --
src/nf_modules/htseq/htseq.config | 2 --
src/nf_modules/kallisto/indexing.config | 2 --
src/nf_modules/kallisto/mapping_paired.config | 2 --
src/nf_modules/kallisto/mapping_single.config | 2 --
src/nf_modules/macs2/peak_calling.config | 2 --
src/nf_modules/multiqc/multiqc_paired.config | 2 --
src/nf_modules/multiqc/multiqc_single.config | 2 --
src/nf_modules/music/peak_calling_single.config | 2 --
src/nf_modules/rsem/indexing.config | 2 --
src/nf_modules/rsem/quantification_paired.config | 2 --
src/nf_modules/rsem/quantification_single.config | 2 --
src/nf_modules/sambamba/index_bams.config | 2 --
src/nf_modules/sambamba/sort_bams.config | 2 --
src/nf_modules/sambamba/split_bams.config | 2 --
src/nf_modules/samblaster/dedup_sams.config | 2 --
src/nf_modules/samtools/filter_bams.config | 2 --
src/nf_modules/samtools/index_bams.config | 2 --
src/nf_modules/samtools/sort_bams.config | 2 --
src/nf_modules/samtools/split_bams.config | 2 --
src/nf_modules/sratoolkit/fastqdump.config | 2 --
src/nf_modules/star/indexing.config | 2 --
src/nf_modules/star/mapping_paired.config | 2 --
src/nf_modules/star/mapping_single.config | 2 --
src/nf_modules/subread/subread.config | 2 --
src/nf_modules/urqt/trimming_paired.config | 2 --
src/nf_modules/urqt/trimming_single.config | 2 --
src/solution_RNASeq.config | 14 --------------
49 files changed, 1 insertion(+), 109 deletions(-)
diff --git a/src/.update_config.sh b/src/.update_config.sh
index 0beb2b1b..2ea29fcf 100644
--- a/src/.update_config.sh
+++ b/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 {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 6b642d67..a04494e6 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/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
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 56d24810..ccf47042 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/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"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 7f564233..e6c7c6da 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/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
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 7f564233..e6c7c6da 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/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
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 5248f81c..773c5eae 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/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
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index e3d7b7c6..b9f515f1 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/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
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index e3d7b7c6..b9f515f1 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/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
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index ba8af39e..b3b90059 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/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
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 94f3904d..b28e5b9c 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/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
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8eb32108..02b23b55 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/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
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8eb32108..02b23b55 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/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
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 0d27d53f..839bce09 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/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
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 0d27d53f..839bce09 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/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
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 99461159..9dd57e69 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/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
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 36279710..8c9c1b7a 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/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
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 627384e0..93207846 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/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
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 4545a988..dc9bf8cd 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/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
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 4545a988..dc9bf8cd 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/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
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index fb8c8b2e..5f12694b 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/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
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index fb8c8b2e..5f12694b 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/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
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 074e5311..5d154dd4 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/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"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 354c2607..931ca784 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/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
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 3b60bf84..52d83cf2 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/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
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index a74e8ea3..839ae331 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/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
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index a74e8ea3..839ae331 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/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
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index e272f038..d3cbbdb9 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/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
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 370a3e06..c8fe4a1d 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/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
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6926341d..641a65e3 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/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
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 16df88bc..dea6fa7b 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/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
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 004755f5..86f57dde 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/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
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 3570af32..a959b00f 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/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
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 3570af32..a959b00f 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/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
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index baa6c562..da8f84fc 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/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
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 17ed79c4..61057327 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/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
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 3394ef09..e9df7d69 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/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
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index bb2612c6..e35185c1 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/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
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index a5cce9de..dfd7f8bf 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/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
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index fb362480..173af8fe 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/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
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index c1ee3f37..48f18580 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/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
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6507405f..757a946a 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/samtools:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index e0708d7a..4287e92f 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastq_dump {
container = "lbmc/sratoolkit:2.8.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index d3d5edae..503c1b8c 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 2787b425..d9d43b94 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 2787b425..d9d43b94 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 715e6136..2d09601a 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -34,8 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/subread:1.6.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index e740020e..f5ca8084 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 8df07c4e..374112e5 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index 77142cab..fadfceb4 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -58,9 +58,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -71,8 +68,6 @@ profiles {
withName: trimming {
container = "lbmc/urqt:d62c1f8"
scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
@@ -84,9 +79,6 @@ profiles {
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -96,9 +88,6 @@ profiles {
}
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
@@ -109,9 +98,6 @@ profiles {
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
--
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