diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7230e0a448f5e71bee117993ec421d8701118918..aa59cf49a1fe9b6e656e3f00be78104488138fb7 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 aca112597cee0d5b3b5147096c3420e2df1ea174..91a0fc567e3161c0102f61bdf3b23f75b7d14629 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 b3c8e31c77d95a11932c0635b36fa84fbe61a240..d33ae6c6704b0b954192a55ff0a3c89b1b3affda 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 b3c8e31c77d95a11932c0635b36fa84fbe61a240..d33ae6c6704b0b954192a55ff0a3c89b1b3affda 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 597f971cd9164c188b6107e1b9c82e5ebc32e729..8c5742cfaf6aa8f62df57f329ea753a50f353439 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 10dcb684cbb6d61d6131c2d0594424c5d8444d43..a5c9b8275bedff97407ca649df29fb55dc8fbb29 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 10dcb684cbb6d61d6131c2d0594424c5d8444d43..a5c9b8275bedff97407ca649df29fb55dc8fbb29 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 6f01a5001535d8ccf9b70d6e365ddc0f164d23e8..a8e7a27e8f948af09c793f91b6d1ff19f6775886 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 d475bf7a76d69c96fb4a17e3e6c5c20f69c1b34f..b0a49229d928c0cacb22750913416a135bada978 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 852779a8ca7cca7c07d90d52e761dc7c7b5df20e..2dd2681e93c4d0190ecc3166c8a4d555fc1e065b 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 852779a8ca7cca7c07d90d52e761dc7c7b5df20e..2dd2681e93c4d0190ecc3166c8a4d555fc1e065b 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 3dfeb1835646c7e8067fd02277b5ef7b91fd32e3..2c8c65a1ab9810cc76cbacbe473df7ed5901eace 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 3dfeb1835646c7e8067fd02277b5ef7b91fd32e3..2c8c65a1ab9810cc76cbacbe473df7ed5901eace 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 b5276da8d418c7ad2404803a7275075e188e2bac..720561761b5a86ad3621715d33c39fc30f4994f6 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 55c03e3f12166d0c7fe3a4b93e90e075454a83f9..3eb067b5b3fd784d360a7eb260624fd412105151 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 2dd2466506b53f3f7d420f3fabd0222b899b36ad..7068f94cc72eec6ce5d58091f70c107811df4ca3 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 c8a289fad4885c1987a8637c441a532ab71b1f39..c2fcafa50122098aaa954a9035fc265293e2cdff 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 c8a289fad4885c1987a8637c441a532ab71b1f39..c2fcafa50122098aaa954a9035fc265293e2cdff 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 1c02c54830961ec16aec0f0e37c0127e31df1ed6..75d352bc541fcfe51bff9ffdf4a7aa480a42cd58 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 1c02c54830961ec16aec0f0e37c0127e31df1ed6..75d352bc541fcfe51bff9ffdf4a7aa480a42cd58 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 db0217aa45eb268ef4516a9c7853a311dcdaa96c..80cf1ea07350ed7befe6be965b424a1088d99f49 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 d496d8608fa3c7791eaf6171a78e9e80cf07201f..e0d73fc288afc9d5875210ea52a7f949d4713880 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 d496d8608fa3c7791eaf6171a78e9e80cf07201f..e0d73fc288afc9d5875210ea52a7f949d4713880 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 d20648c740c0ea0538ff20ec70b13bc02b1e9a12..cc6255c246351edf8a97d9b0ea05cc788a9b6cf2 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 5b126bbe50713c058be01968e1cebe144e492443..d5783a2b0b4bd3e3be4e296b8a11acd4b95dc55f 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 7680223470d6fad16917d6786252264dc32d0844..175b0f9245a98f55eb1aa08d86601e229b4afb9c 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 7680223470d6fad16917d6786252264dc32d0844..175b0f9245a98f55eb1aa08d86601e229b4afb9c 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 18b639e7d5c14fd07a75c54a97186823eb772a97..ef11303d8a2dc634668f2f8cf557f0b0630a29f6 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 53442413b98e69e316ada977f08cc04a64efed05..295a824d3c6ec97b49db85dcbd0f1f46f77bdcd8 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 a52a9a4174753ee34628779fbd3abfacbde4f4c8..f43250944db66a534dbf604d90b6f80af366d667 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 613fdc4d6cdfe3e0778b538ceea46373ecb15501..8d00ba922ee6420eb94691b1a6fc0b9ad5a186a8 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 602f8319a647711507b5f11be59353d8f8355ac5..0b40f13bdbb192a4294d8380ed441df03283ce7f 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 9a2f21015b3bbb4959f3b7fa673f2ecd9fea981d..15bdaa8a9c950e20ad2ba2b4833a051517ecb431 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 9a2f21015b3bbb4959f3b7fa673f2ecd9fea981d..15bdaa8a9c950e20ad2ba2b4833a051517ecb431 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 6de14fb09a50c5668b72afeaa82b202ee931d1e6..7d19d20b56e4c35d628ffefe5bc248d0300f2da8 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 ed485d3ea604f3bfc5b7f447da6c6ed2d54eb319..c77b4b322d9f610101bd2876b64ae8a2e3f4c8ca 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 78752eddd679dbb81bd23e3ad748c7f0280b2666..b37dade1565062bf719c3bded5081e660889c495 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 e850a3fff71c0b9a30f6a52c10fc73aa1121001e..08a0a6330cd95d57980f063197c2ad5a615d9276 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 53b8e45f1b2671c386632a59c8e6a1067d422f40..06a63e48ea78bb5ad53eecaffc77228cf8c77afc 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 692cd174369a32c3229f8becb680a9da1efb43f3..09e97bb49b792c4301756b5b311b4bcfeb07177f 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 9955a3532c199e719d0c3939cc6824006f8205a8..0cb3bf1f9f91dc93b77fb168c7ac4c5fc6c95a68 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 fcb6c20c1e9c317090c919d0ff7489d1c313e8ad..34523d0f72934799a6fde17934045249f856cfcd 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 d6c5b48a3b0cd3f69ebb48a0fc5556afd3a6dbf7..9e6bd1986d32489d78f75243932f2595319bb179 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 e9debde156a26b92faa0f6aa2b8e1b376abfc45c..d08b7b8573db3816598afc421ec90d66d6394ab9 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 3e9227c8c2792acdcb369c353cdcf25a28d72b3d..3f09a7e5f54111e0815cfc9426b750fd76d02a8d 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 34bf633bbc7a1e1db4f41bb10542826eb7a8b3e5..0d2254d56721461a62ef1f91b1851cd6359e4e8c 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"