From 3ced2125795763aad94aea3b19eb96dbfdc2f518 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 5 Nov 2019 17:35:45 +0100
Subject: [PATCH] docker: change config file to use lbmc/ docker repository
---
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/cutadapt/adaptor_removal_paired.config | 2 +-
src/nf_modules/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 | 4 ++--
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/hisat2/mapping_paired.config | 2 +-
src/nf_modules/hisat2/mapping_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/macs2/peak_calling.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/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/subread/subread.config | 4 ++--
src/nf_modules/urqt/trimming_paired.config | 2 +-
src/nf_modules/urqt/trimming_single.config | 2 +-
46 files changed, 53 insertions(+), 53 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1a225212..7230e0a4 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fasta_from_bed {
- container = "bedtools:2.25.0"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 06b57209..aca11259 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: index_fasta {
cpus = 4
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 61f40f9e..b3c8e31c 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 61f40f9e..b3c8e31c 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2d52dc48..597f971c 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 85655e48..10dcb684 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 85655e48..10dcb684 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index c970b5bb..6f01a500 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "bwa:0.7.17"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index af4f9683..d475bf7a 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bwa:0.7.17"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8add46ca..852779a8 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8add46ca..852779a8 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 721d8805..3dfeb183 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 721d8805..3dfeb183 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 5be6a4cb..b5276da8 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "sambamba:0.6.7"
+ container = "lbmc/sambamba:0.6.7"
cpus = 4
}
withName: bam_to_bigwig {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index b0986769..55c03e3f 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: compute_matrix {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index e9fe1504..2dd24665 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: plot_profile {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index df041cb9..c8a289fa 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastp_fastq {
- container = "fastp:0.19.7"
+ container = "lbmc/fastp:0.19.7"
cpus = 1
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index df041cb9..c8a289fa 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastp_fastq {
- container = "fastp:0.19.7"
+ container = "lbmc/fastp:0.19.7"
cpus = 1
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 2ed15c54..1c02c548 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 2ed15c54..1c02c548 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index d97e7c74..db0217aa 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
cpus = 4
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index c0b9c808..d496d860 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index c0b9c808..d496d860 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index a04f0851..d20648c7 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "htseq:0.11.2"
+ container = "lbmc/htseq:0.11.2"
cpus = 1
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b677b616..5b126bbe 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withNamek index_fasta {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 620e506d..76802234 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 620e506d..76802234 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 8e3965f8..18b639e7 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: peak_calling {
- container = "macs2:2.1.2"
+ container = "lbmc/macs2:2.1.2"
cpus = 4
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1825a135..53442413 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -5,11 +5,11 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.7"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6a2edfb6..a52a9a41 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.7"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index dc46d8c8..613fdc4d 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -4,15 +4,15 @@ profiles {
docker.enabled = true
process {
withName: compute_mappability {
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_preprocessing {
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_computation{
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d58a310d..602f8319 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 75aae6ed..9a2f2101 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 75aae6ed..9a2f2101 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 9199b7a4..6de14fb0 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 0a71fc38..ed485d3e 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 8a3e4ab5..78752edd 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: split_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 7fd05167..e850a3ff 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: dedup_sam {
- container = "samblaster:0.1.24"
+ container = "lbmc/samblaster:0.1.24"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index fc7a216c..53b8e45f 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: filter_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 8b910b60..692cd174 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index d5e06e31..9955a353 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index c145bf33..fcb6c20c 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: split_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 2
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index ee6ed1fa..d6c5b48a 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastq_dump {
- container = "sratoolkit:2.8.2"
+ container = "lbmc/sratoolkit:2.8.2"
cpus = 1
}
}
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 19f20463..e9debde1 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "subread:1.6.4"
+ container = "lbmc/subread:1.6.4"
cpus = 1
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index dbe4e11c..3e9227c8 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: trimming {
cpus = 4
- container = "urqt:d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 016d6503..34bf633b 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "urqt:d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
cpus = 4
}
}
--
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