From 80b5c871fb27c3abdbb1e77df82200fa7e2a7eda Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Mar 2019 15:31:09 +0100
Subject: [PATCH] nf_modules: update config files to match psmn lowercase
module names
---
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 +-
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/fastqc/fastqc_paired.config | 2 +-
src/nf_modules/fastqc/fastqc_single.config | 2 +-
src/nf_modules/htseq/htseq.config | 4 ++--
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/multiqc/multiqc_paired.config | 4 ++--
src/nf_modules/multiqc/multiqc_single.config | 4 ++--
src/nf_modules/music/peak_calling_single.config | 6 +++---
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/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/urqt/trimming_paired.config | 2 +-
src/nf_modules/urqt/trimming_single.config | 2 +-
31 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 5311e9f5..c1ac99f1 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "BEDtools/2.25.0"
+ module = "bedtools/2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 5e9d8233..9ae43af6 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie/1.2.2"
+ module = "bowtie/1.2.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index b27917e1..e516bc30 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie/1.2.2:SAMtools/1.7"
+ module = "bowtie/1.2.2:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index b27917e1..e516bc30 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie/1.2.2:SAMtools/1.7"
+ module = "bowtie/1.2.2:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index c53d855a..0589f4dd 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie2/2.3.4.1"
+ module = "bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 27933c3b..eee236b7 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+ module = "bowtie2/2.3.4.1:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 27933c3b..eee236b7 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+ module = "bowtie2/2.3.4.1:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 367e0dfd..aa5967be 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "BWA/0.7.17"
+ module = "bwa/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 5535fd10..e71fc949 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "BWA/0.7.17"
+ module = "bwa/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index c1b71cb0..ab28edcb 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -25,7 +25,7 @@ profiles {
}
withName: bam_to_bigwig {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "deepTools/3.0.2"
+ module = "deeptools/3.0.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 27e63ca6..7159cbc7 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: compute_matrix {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "deepTools/3.0.2"
+ module = "deeptools/3.0.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 4a94d1de..984575cc 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: plot_profile {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "deepTools/3.0.2"
+ module = "deeptools/3.0.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 94baaa28..78abe927 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "FastQC/0.11.5"
+ module = "fastqc/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 94baaa28..78abe927 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "FastQC/0.11.5"
+ module = "fastqc/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 87368e13..94fe2781 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -15,7 +15,7 @@ profiles {
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SAMtools/1.7"
+ module = "samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
@@ -24,7 +24,7 @@ profiles {
}
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "HTSeq/0.8.0"
+ module = "htseq/0.8.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index c52f9b51..8e713129 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Kallisto/0.44.0"
+ module = "kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 2274d13d..a0ec051d 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Kallisto/0.44.0"
+ module = "kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 2274d13d..a0ec051d 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "Kallisto/0.44.0"
+ module = "kallisto/0.44.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 592b63c2..323e81d2 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -16,7 +16,7 @@ profiles {
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "FastQC/0.11.5"
+ module = "fastqc/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
@@ -27,7 +27,7 @@ profiles {
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "MultiQC/1.0"
+ module = "multiqc/1.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 7f6bf3d9..a7f3e82e 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -15,7 +15,7 @@ profiles {
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "FastQC/0.11.5"
+ module = "fastqc/0.11.5"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
@@ -26,7 +26,7 @@ profiles {
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "MultiQC/1.0"
+ module = "multiqc/1.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 2d7145ae..f9a1d799 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -18,7 +18,7 @@ profiles {
process{
withName: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "MUSIC/6613c53"
+ module = "music/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
@@ -27,7 +27,7 @@ profiles {
}
withName: music_preprocessing {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "MUSIC/6613c53"
+ module = "music/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
@@ -36,7 +36,7 @@ profiles {
}
withName: music_computation {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "MUSIC/6613c53"
+ module = "music/6613c53"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index c0d3287e..059dbbaa 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "RSEM/1.3.0:SAMtools/1.7"
+ module = "rsem/1.3.0:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 46ff1549..16de29e8 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "RSEM/1.3.0:SAMtools/1.7"
+ module = "rsem/1.3.0:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 46ff1549..16de29e8 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "RSEM/1.3.0:SAMtools/1.7"
+ module = "rsem/1.3.0:samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "30GB"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index ef3aa491..36d191dc 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: filter_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SAMtools/1.7"
+ module = "samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 135b6b3a..fc6122c9 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SAMtools/1.7"
+ module = "samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 1c1bdca5..0071ca2c 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SAMtools/1.7"
+ module = "samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 15880281..e2d521ce 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SAMtools/1.7"
+ module = "samtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 67676b9a..ef335129 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -12,7 +12,7 @@ profiles {
process{
withName: fastq_dump {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "SRAtoolkit/2.8.2"
+ module = "sratoolkit/2.8.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index c2b4e3f6..ce5d5736 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "UrQt/d62c1f8"
+ module = "urqt/d62c1f8"
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index b102d8bd..74503ba1 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -22,7 +22,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "UrQt/d62c1f8"
+ module = "urqt/d62c1f8"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
--
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