From 0d93daf3893edf6db7535b5842c167e0d01b3d62 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 5 Nov 2019 18:40:37 +0100
Subject: [PATCH] singularity: update configs to use docker hub and specified
cacheDir
---
src/nf_modules/bedtools/fasta_from_bed.config | 6 ++++--
src/nf_modules/bowtie/indexing.config | 6 ++++--
src/nf_modules/bowtie/mapping_paired.config | 6 ++++--
src/nf_modules/bowtie/mapping_single.config | 6 ++++--
src/nf_modules/bowtie2/indexing.config | 6 ++++--
src/nf_modules/bowtie2/mapping_paired.config | 6 ++++--
src/nf_modules/bowtie2/mapping_single.config | 6 ++++--
src/nf_modules/bwa/indexing.config | 6 ++++--
src/nf_modules/bwa/mapping_paired.config | 6 ++++--
.../cutadapt/adaptor_removal_paired.config | 6 ++++--
.../cutadapt/adaptor_removal_single.config | 6 ++++--
src/nf_modules/cutadapt/trimming_paired.config | 6 ++++--
src/nf_modules/cutadapt/trimming_single.config | 6 ++++--
src/nf_modules/deeptools/bam_to_bigwig.config | 10 ++++++----
src/nf_modules/deeptools/compute_matrix.config | 6 ++++--
src/nf_modules/deeptools/plot_profile.config | 6 ++++--
src/nf_modules/fastp/fastp_paired.config | 6 ++++--
src/nf_modules/fastp/fastp_single.config | 6 ++++--
src/nf_modules/fastqc/fastqc_paired.config | 6 ++++--
src/nf_modules/fastqc/fastqc_single.config | 6 ++++--
src/nf_modules/hisat2/indexing.config | 6 ++++--
src/nf_modules/hisat2/mapping_paired.config | 6 ++++--
src/nf_modules/hisat2/mapping_single.config | 6 ++++--
src/nf_modules/htseq/htseq.config | 10 ++++++----
src/nf_modules/kallisto/indexing.config | 6 ++++--
src/nf_modules/kallisto/mapping_paired.config | 6 ++++--
src/nf_modules/kallisto/mapping_single.config | 6 ++++--
src/nf_modules/macs2/peak_calling.config | 6 ++++--
src/nf_modules/multiqc/multiqc_paired.config | 10 ++++++----
src/nf_modules/multiqc/multiqc_single.config | 10 ++++++----
src/nf_modules/music/peak_calling_single.config | 14 ++++++++------
src/nf_modules/rsem/indexing.config | 6 ++++--
src/nf_modules/rsem/quantification_paired.config | 6 ++++--
src/nf_modules/rsem/quantification_single.config | 6 ++++--
src/nf_modules/sambamba/index_bams.config | 6 ++++--
src/nf_modules/sambamba/sort_bams.config | 6 ++++--
src/nf_modules/sambamba/split_bams.config | 6 ++++--
src/nf_modules/samblaster/dedup_sams.config | 6 ++++--
src/nf_modules/samtools/filter_bams.config | 6 ++++--
src/nf_modules/samtools/index_bams.config | 6 ++++--
src/nf_modules/samtools/sort_bams.config | 6 ++++--
src/nf_modules/samtools/split_bams.config | 6 ++++--
src/nf_modules/sratoolkit/fastqdump.config | 6 ++++--
src/nf_modules/subread/subread.config | 10 ++++++----
src/nf_modules/urqt/trimming_paired.config | 6 ++++--
src/nf_modules/urqt/trimming_single.config | 6 ++++--
46 files changed, 198 insertions(+), 106 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7230e0a4..aa59cf49 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fasta_from_bed {
- container = "file://bin/bedtools:2.25.0.img"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fasta_from_bed {
- container = "/sps/lbmc/common/singularity/bedtools:2.25.0.img"
+ container = "lbmc/bedtools:2.25.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index aca11259..91a0fc56 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
cpus = 4
- container = "file://bin/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index b3c8e31c..d33ae6c6 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index b3c8e31c..d33ae6c6 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
+ container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 597f971c..8c5742cf 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 10dcb684..a5c9b827 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 10dcb684..a5c9b827 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 6f01a500..a8e7a27e 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
- container = "file://bin/bwa:0.7.17.img"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity//bwa:0.7.17.img"
+ container = "lbmc/bwa:0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index d475bf7a..b0a49229 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/bwa:0.7.17.img"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
+ container = "lbmc/bwa:0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 852779a8..2dd2681e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "file://bin/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
- container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 852779a8..2dd2681e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "file://bin/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
- container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 3dfeb183..2c8c65a1 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "file://bin/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -49,10 +50,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 3dfeb183..2c8c65a1 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "file://bin/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -49,10 +50,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
+ container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index b5276da8..72056176 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -15,13 +15,14 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_bam {
- container = "file://bin/sambamba:0.6.7.img"
+ container = "lbmc/sambamba:0.6.7"
cpus = 4
}
withName: bam_to_bigwig {
- container = "file://bin/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
@@ -82,10 +83,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
- container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+ container = "lbmc/sambamba:0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -96,7 +98,7 @@ profiles {
queue = 'huge'
}
withName: bam_to_bigwig {
- container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 55c03e3f..3eb067b5 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: compute_matrix {
- container = "file://bin/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: compute_matrix {
- container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 2dd24665..7068f94c 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: compute_matrix {
- container = "file://bin/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: plot_profile {
- container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
+ container = "lbmc/deeptools:3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index c8a289fa..c2fcafa5 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastp_fastq {
cpus = 1
- container = "file://bin/fastp:0.19.7.img"
+ container = "lbmc/fastp:0.19.7"
}
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
- container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+ container = "lbmc/fastp:0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index c8a289fa..c2fcafa5 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastp_fastq {
cpus = 1
- container = "file://bin/fastp:0.19.7.img"
+ container = "lbmc/fastp:0.19.7"
}
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
- container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
+ container = "lbmc/fastp:0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 1c02c548..75d352bc 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastqc_fastq {
cpus = 1
- container = "file://bin/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
}
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastqc_fastq {
- container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 1c02c548..75d352bc 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastqc_fastq {
cpus = 1
- container = "file://bin/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
}
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastqc_fastq {
- container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index db0217aa..80cf1ea0 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
cpus = 4
- container = "file://bin/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index d496d860..e0d73fc2 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index d496d860..e0d73fc2 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
+ container = "lbmc/hisat2:2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index d20648c7..cc6255c2 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -15,13 +15,14 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: sort_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "file://bin/htseq:0.11.2.img"
+ container = "lbmc/htseq:0.11.2"
cpus = 1
}
}
@@ -80,10 +81,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -94,7 +96,7 @@ profiles {
queue = 'huge'
}
withName: counting {
- container = "/sps/lbmc/common/singularity/htseq:0.11.2.img"
+ container = "lbmc/htseq:0.11.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 5b126bbe..d5783a2b 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
- container = "file://bin/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 76802234..175b0f92 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 76802234..175b0f92 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 18b639e7..ef11303d 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: peak_calling {
- container = "file://bin/macs2:2.1.2.img"
+ container = "lbmc/macs2:2.1.2"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: peak_calling {
- container = "/sps/lbmc/common/singularity/macs2:2.1.2.img"
+ container = "lbmc/macs2:2.1.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 53442413..295a824d 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -16,13 +16,14 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastqc_fastq {
- container = "file://bin/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.7.img"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
@@ -85,10 +86,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_fastqc {
- container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -99,7 +101,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+ container = "lbmc/multiqc:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index a52a9a41..f4325094 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -15,13 +15,14 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: fastqc_fastq {
- container = "file://bin/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.7.img"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
@@ -84,10 +85,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_fastqc {
- container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ container = "lbmc/fastqc:0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -98,7 +100,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
+ container = "lbmc/multiqc:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 613fdc4d..8d00ba92 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -19,17 +19,18 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: compute_mappability {
- container = "file://bin/music:6613c53.img"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_preprocessing {
- container = "file://bin/music:6613c53.img"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_computation{
- container = "file://bin/music:6613c53.img"
+ container = "lbmc/music:6613c53"
cpus = 1
}
}
@@ -110,10 +111,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: compute_mappability {
- container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ container = "lbmc/music:6613c53"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -124,7 +126,7 @@ profiles {
queue = 'huge'
}
withName: music_preprocessing {
- container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ container = "lbmc/music:6613c53"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -135,7 +137,7 @@ profiles {
queue = 'huge'
}
withName: music_computation{
- container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ container = "lbmc/music:6613c53"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 602f8319..0b40f13b 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_fasta {
- container = "file://bin/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 9a2f2101..15bdaa8a 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 9a2f2101..15bdaa8a 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: mapping_fastq {
- container = "file://bin/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
- container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
+ container = "lbmc/rsem:1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 6de14fb0..7d19d20b 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_bam {
- container = "file://bin/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
- container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index ed485d3e..c77b4b32 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: sort_bam {
- container = "file://bin/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
- container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 78752edd..b37dade1 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: split_bam {
- container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
+ container = "lbmc/sambamba:0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index e850a3ff..08a0a633 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.7.img"
+ container = "lbmc/sambamba:0.6.7"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: dedup_sam {
- container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
+ container = "lbmc/sambamba:0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 53b8e45f..06a63e48 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: filter_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: filter_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 692cd174..09e97bb4 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: index_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 9955a353..0cb3bf1f 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: sort_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index fcb6c20c..34523d0f 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: split_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 2
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: split_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index d6c5b48a..9e6bd198 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: split_bam {
- container = "file://bin/sratoolkit:2.8.2.img"
+ container = "lbmc/sratoolkit:2.8.2"
cpus = 1
}
}
@@ -50,10 +51,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastq_dump {
- container = "/sps/lbmc/common/singularity/sratoolkit:2.8.2.img"
+ container = "lbmc/sratoolkit:2.8.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index e9debde1..d08b7b85 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -15,13 +15,14 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: sort_bam {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "file://bin/subread:1.6.4.img"
+ container = "lbmc/subread:1.6.4"
cpus = 1
}
}
@@ -80,10 +81,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: sort_bam {
- container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -94,7 +96,7 @@ profiles {
queue = 'huge'
}
withName: counting {
- container = "/sps/lbmc/common/singularity/subread:1.6.4.img"
+ container = "lbmc/subread:1.6.4"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 3e9227c8..3f09a7e5 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -11,10 +11,11 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: trimming {
cpus = 4
- container = "file://bin/urqt:d62c1f8.img"
+ container = "lbmc/urqt:d62c1f8"
}
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+ container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 34bf633b..0d2254d5 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -11,9 +11,10 @@ profiles {
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "file://bin/urqt:d62c1f8.img"
+ container = "lbmc/urqt:d62c1f8"
cpus = 4
}
}
@@ -51,10 +52,11 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
+ singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
- container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
+ container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
--
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