From 85a682163fe4fada30e12d92ef901732e7beeb95 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 19 Dec 2018 11:06:18 +0100
Subject: [PATCH] nf_modules: fix withname -> withName in config files
---
src/nf_modules/BWA/indexing.config | 4 ++--
src/nf_modules/BWA/mapping_paired.config | 4 ++--
src/nf_modules/Bowtie/indexing.config | 4 ++--
src/nf_modules/Bowtie/mapping_paired.config | 4 ++--
src/nf_modules/Bowtie/mapping_single.config | 4 ++--
src/nf_modules/Bowtie2/indexing.config | 4 ++--
src/nf_modules/Bowtie2/mapping_paired.config | 4 ++--
src/nf_modules/Bowtie2/mapping_single.config | 4 ++--
src/nf_modules/FastQC/fastqc_paired.config | 4 ++--
src/nf_modules/FastQC/fastqc_single.config | 4 ++--
src/nf_modules/HTSeq/htseq.config | 8 ++++----
src/nf_modules/MUSIC/peak_calling_single.config | 12 ++++++------
src/nf_modules/MultiQC/multiqc_paired.config | 8 ++++----
src/nf_modules/MultiQC/multiqc_single.config | 8 ++++----
src/nf_modules/RSEM/indexing.config | 4 ++--
src/nf_modules/RSEM/quantification_paired.config | 4 ++--
src/nf_modules/RSEM/quantification_single.config | 4 ++--
src/nf_modules/SAMtools/filter_bams.config | 4 ++--
src/nf_modules/SAMtools/index_bams.config | 4 ++--
src/nf_modules/SAMtools/sort_bams.config | 4 ++--
src/nf_modules/SAMtools/split_bams.config | 4 ++--
src/nf_modules/SRAtoolkit/fastqdump.config | 4 ++--
src/nf_modules/sambamba/index_bams.config | 4 ++--
src/nf_modules/sambamba/sort_bams.config | 4 ++--
src/nf_modules/sambamba/split_bams.config | 4 ++--
src/nf_modules/samblaster/dedup_sams.config | 4 ++--
26 files changed, 62 insertions(+), 62 deletions(-)
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index acc8e539..2936204f 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_fasta {
+ withName: index_fasta {
container = "bwa:0.7.17"
}
}
}
psmn {
process{
- withname: index_fasta {
+ withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BWA/0.7.17"
executor = "sge"
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index 808e12a6..ce8f7f45 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bwa:0.7.17"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BWA/0.7.17"
executor = "sge"
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index a1b6addd..954b245e 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_fasta {
+ withName: index_fasta {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- withname: index_fasta {
+ withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie/1.2.2"
executor = "sge"
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index 9d661f3f..5b3b9f95 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index 9d661f3f..5b3b9f95 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 82ebc902..434889bc 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
executor = "sge"
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 8fe161a0..30150ff9 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 8fe161a0..30150ff9 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index b16c5d07..9fda3d13 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/src/nf_modules/FastQC/fastqc_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
psmn {
process{
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
executor = "sge"
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index b16c5d07..9fda3d13 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
psmn {
process{
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
executor = "sge"
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
index 95919f56..87368e13 100644
--- a/src/nf_modules/HTSeq/htseq.config
+++ b/src/nf_modules/HTSeq/htseq.config
@@ -3,17 +3,17 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: sort_bam {
+ withName: sort_bam {
container = "samtools:1.7"
}
- withname: counting {
+ withName: counting {
container = "htseq:0.8.0"
}
}
}
psmn {
process{
- withname: sort_bam {
+ withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
@@ -22,7 +22,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
- withname: trimming {
+ withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "HTSeq/0.8.0"
executor = "sge"
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index f8ad13e2..2d7145ae 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/src/nf_modules/MUSIC/peak_calling_single.config
@@ -3,20 +3,20 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: compute_mappability {
+ withName: compute_mappability {
container = "music:6613c53"
}
- withname: music_preprocessing {
+ withName: music_preprocessing {
container = "music:6613c53"
}
- withname: music_computation {
+ withName: music_computation {
container = "music:6613c53"
}
}
}
psmn {
process{
- withname: compute_mappability {
+ withName: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
executor = "sge"
@@ -25,7 +25,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
- withname: music_preprocessing {
+ withName: music_preprocessing {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
executor = "sge"
@@ -34,7 +34,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
- withname: music_computation {
+ withName: music_computation {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
executor = "sge"
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index d986c1f0..592b63c2 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/src/nf_modules/MultiQC/multiqc_paired.config
@@ -4,17 +4,17 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
container = "fastqc:0.11.5"
}
- withname: multiqc {
+ withName: multiqc {
container = "multiqc:1.0"
}
}
}
psmn {
process{
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
executor = "sge"
@@ -25,7 +25,7 @@ profiles {
pollInterval = '60sec'
queue = 'monointeldeb128'
}
- withname: multiqc {
+ withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0"
executor = "sge"
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index a6a2948a..7f6bf3d9 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -3,17 +3,17 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
container = "fastqc:0.11.5"
}
- withname: multiqc {
+ withName: multiqc {
container = "multiqc:1.0"
}
}
}
psmn {
process{
- withname: fastqc_fastq {
+ withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
executor = "sge"
@@ -24,7 +24,7 @@ profiles {
pollInterval = '60sec'
queue = 'monointeldeb128'
}
- withname: multiqc {
+ withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0"
executor = "sge"
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
index d6d0a908..c0d3287e 100644
--- a/src/nf_modules/RSEM/indexing.config
+++ b/src/nf_modules/RSEM/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_fasta {
+ withName: index_fasta {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- withname: index_fasta {
+ withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
index 0801e388..46ff1549 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
index 0801e388..46ff1549 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: mapping_fastq {
+ withName: mapping_fastq {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- withname: mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index a000c5cd..ef3aa491 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: filter_bam {
+ withName: filter_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- withname: filter_bam {
+ withName: filter_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
index c44c2e73..135b6b3a 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_bam {
+ withName: index_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- withname: index_bam {
+ withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
index c0e08d02..1c1bdca5 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: sort_bam {
+ withName: sort_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- withname: sort_bam {
+ withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
index 3ef8321e..15880281 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: split_bam {
+ withName: split_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- withname: split_bam {
+ withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
executor = "sge"
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index edd7856a..67676b9a 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: fastq_dump {
+ withName: fastq_dump {
container = "sratoolkit:2.8.2"
}
}
}
psmn {
process{
- withname: fastq_dump {
+ withName: fastq_dump {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SRAtoolkit/2.8.2"
executor = "sge"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 6bbae437..22fc18de 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_bam {
+ withName: index_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- withname: index_bam {
+ withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "sambamba/0.6.7"
executor = "sge"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index c60ee44e..9dd63fca 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: sort_bam {
+ withName: sort_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- withname: sort_bam {
+ withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "sambamba/0.6.7"
executor = "sge"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 51afa4fa..3b9acd72 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: split_bam {
+ withName: split_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- withname: split_bam {
+ withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "sambamba/0.6.7"
executor = "sge"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 6aeaec5f..42e3757c 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: dedup_sam {
+ withName: dedup_sam {
container = "samblaster:0.1.24"
}
}
}
psmn {
process{
- withname: dedup_sam {
+ withName: dedup_sam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "samblaster/0.1.24"
executor = "sge"
--
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