diff --git a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
index c993e745ee294fc3ddb4601f850dd401b1f6b176..1649aeedd22d978ce3591e3b2c227abf1e3aa2be 100644
--- a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
+++ b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
@@ -4,7 +4,7 @@ MAINTAINER Laurent Modolo
ENV B_VERSION=0.39.3
ENV K_VERSION=0.46.1
-RUN apk add --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf && \
+RUN apk add --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf bash && \
wget https://github.com/BUStools/bustools/archive/v${B_VERSION}.tar.gz && \
tar xvf v${B_VERSION}.tar.gz && \
cd bustools-${B_VERSION} && \
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index a04494e663516f7643d786da08e7e6229a5b4f37..077270d718912d8430da8a86380ebafe4fb02ea4 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bedtools/fasta_from_bed.nf b/src/nf_modules/bedtools/fasta_from_bed.nf
index 5e7504dcd35f29e44964e629ef8fba894c633224..85dce5556bb9a583d0dd70dadcdef635ce842074 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.nf
+++ b/src/nf_modules/bedtools/fasta_from_bed.nf
@@ -24,6 +24,7 @@ Channel
process fasta_from_bed {
tag "${bed.baseName}"
publishDir "results/fasta/", mode: 'copy'
+ label "bedtools"
input:
file fasta from fasta_files
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index ccf47042bc019c4d8a601543ec7bc7213cbb738c..50dff96596a72ad4f568698ef4a80df9e0b85d1b 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: index_fasta {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/indexing.nf b/src/nf_modules/bowtie/indexing.nf
index cf6bfaee07c7f81abb3b5b8a56fa526c24c67215..d09a5de8676bc85e43a0ac76a7dbcdbc5df50f9e 100644
--- a/src/nf_modules/bowtie/indexing.nf
+++ b/src/nf_modules/bowtie/indexing.nf
@@ -12,6 +12,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "bowtie"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index e6c7c6dadd4625a6affeabcfc68e50aa30f8f227..1d924e9b23430cc81c0f1576ad9d6bf78ebf755e 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
index 90b47ba41994003c42653cc40f1736513100d76f..6357a8b69de5cc083dba8451964c1848a939e0c2 100644
--- a/src/nf_modules/bowtie/mapping_paired.nf
+++ b/src/nf_modules/bowtie/mapping_paired.nf
@@ -20,6 +20,7 @@ Channel
process mapping_fastq {
tag "$pair_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index e6c7c6dadd4625a6affeabcfc68e50aa30f8f227..1d924e9b23430cc81c0f1576ad9d6bf78ebf755e 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_single.nf b/src/nf_modules/bowtie/mapping_single.nf
index 268bdfa85071a766c027aa518e38bcfc4778b303..ac28719368de4e9055c98bf138ae33df81708004 100644
--- a/src/nf_modules/bowtie/mapping_single.nf
+++ b/src/nf_modules/bowtie/mapping_single.nf
@@ -20,6 +20,7 @@ Channel
process mapping_fastq {
tag "$file_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 773c5eae572785d6a7fea6ed1e3ccb9b8d14e00d..5a487f8e02c0d48dc586f68c1de1616e87669dd6 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/indexing.nf b/src/nf_modules/bowtie2/indexing.nf
index 45318049b076f6dcad4d7ef2335185796a5e7234..e1ec9ae97a0e26495e674b9319960eb363fd33fa 100644
--- a/src/nf_modules/bowtie2/indexing.nf
+++ b/src/nf_modules/bowtie2/indexing.nf
@@ -10,6 +10,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "bowtie2"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index b9f515f11cbc300b8208d7033a90f40bb75ef774..addc6b2e3722f35ceffda826c6121f89dc4761ee 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_paired.nf b/src/nf_modules/bowtie2/mapping_paired.nf
index 225508d88449f0141775902092b1fb4e4e57ffc2..96c209fdb0f8aca424adf6a5ef8cd7a2a23a3912 100644
--- a/src/nf_modules/bowtie2/mapping_paired.nf
+++ b/src/nf_modules/bowtie2/mapping_paired.nf
@@ -16,6 +16,7 @@ Channel
process mapping_fastq {
tag "$pair_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie2"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index b9f515f11cbc300b8208d7033a90f40bb75ef774..addc6b2e3722f35ceffda826c6121f89dc4761ee 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_single.nf b/src/nf_modules/bowtie2/mapping_single.nf
index b5bfff2b11cdb837f216b0b1a245587c486c84d2..69db77e2f7fb40c2bc00ba663619ef6640b34df3 100644
--- a/src/nf_modules/bowtie2/mapping_single.nf
+++ b/src/nf_modules/bowtie2/mapping_single.nf
@@ -16,6 +16,7 @@ Channel
process mapping_fastq {
tag "$file_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie2"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index ea069fd8c3e413f1bc28bad77b6d427b1f41e29f..33b2179fd41d2a43e1001d6b75df343b879f94be 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/adaptor_removal_paired.nf
index f78d5c2dab0c8a83fd105c5eaddbbc1fd8c4e13e..0d20373335c963833d71f1d9d12fd0145b004db1 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.nf
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.nf
@@ -8,6 +8,7 @@ Channel
process adaptor_removal {
tag "$pair_id"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+ label "cutadapt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index ea069fd8c3e413f1bc28bad77b6d427b1f41e29f..33b2179fd41d2a43e1001d6b75df343b879f94be 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.nf b/src/nf_modules/cutadapt/adaptor_removal_single.nf
index 26f3cd7602bf242f718a027bad253ba2fe1e8d8c..ac2b631ef4029ea635174014b15fe0665113f595 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.nf
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.nf
@@ -8,6 +8,7 @@ Channel
process adaptor_removal {
tag "$file_id"
+ label "cutadapt"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index d69a7021effe93ae0c3ede2c8b2f9adc05362025..33b2179fd41d2a43e1001d6b75df343b879f94be 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_paired.nf b/src/nf_modules/cutadapt/trimming_paired.nf
index 704240f46818b79a540e71273fc1512216d109e6..9fb317ffbddec30204fb940b011a8abbade98e73 100644
--- a/src/nf_modules/cutadapt/trimming_paired.nf
+++ b/src/nf_modules/cutadapt/trimming_paired.nf
@@ -8,6 +8,7 @@ Channel
process trimming {
tag "$pair_id"
publishDir "results/fastq/trimming/", mode: 'copy'
+ label "cutadapt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index d69a7021effe93ae0c3ede2c8b2f9adc05362025..33b2179fd41d2a43e1001d6b75df343b879f94be 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_single.nf b/src/nf_modules/cutadapt/trimming_single.nf
index 9b3764dbed4dd51bfb361b56b4f5fc737b18c270..0d125e7e987c0a1ffaca54dfef63a497205d7d33 100644
--- a/src/nf_modules/cutadapt/trimming_single.nf
+++ b/src/nf_modules/cutadapt/trimming_single.nf
@@ -8,6 +8,7 @@ Channel
process trimming {
tag "$file_id"
+ label "cutadapt"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 52d83cf298c9daee3d767a8b93ba6be28076d3e2..1f3f39e8744f3788807dc409ed567f543784995b 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName index_fasta {
+ withLabel kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
index ea153569693b5dd057727a072d14dadd0ce77bf5..5b0fba5e5502b5ee3c3d10b3697233a594cec0ac 100644
--- a/src/nf_modules/kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -10,6 +10,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "kallisto"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 839ae33192e5c9ca4c72ff83f64e89abed05d5ac..962e1fdc923692b4395d72dfee42ec80001861b1 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_paired.nf b/src/nf_modules/kallisto/mapping_paired.nf
index 455e70cd4030a28e9fe3fcaccadc92e915c75859..56f130005a530684a26280143aea7c82652ea332 100644
--- a/src/nf_modules/kallisto/mapping_paired.nf
+++ b/src/nf_modules/kallisto/mapping_paired.nf
@@ -16,6 +16,7 @@ Channel
process mapping_fastq {
tag "$reads"
publishDir "results/mapping/quantification/", mode: 'copy'
+ label "kallisto"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 839ae33192e5c9ca4c72ff83f64e89abed05d5ac..962e1fdc923692b4395d72dfee42ec80001861b1 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_single.nf b/src/nf_modules/kallisto/mapping_single.nf
index 95bed86418491de0f8038a23c14c6b75eb973d55..7ae2128012fccab58732ca8b8781833b325da586 100644
--- a/src/nf_modules/kallisto/mapping_single.nf
+++ b/src/nf_modules/kallisto/mapping_single.nf
@@ -21,6 +21,7 @@ Channel
process mapping_fastq {
tag "$file_id"
publishDir "results/mapping/quantification/", mode: 'copy'
+ label "kallisto"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index f5ca80843af2ead8ca438a839765a77497e7a337..f8f533f4fc03fd1e5a2f862641f68e1764658e41 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: urqt {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: urqt {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_paired.nf b/src/nf_modules/urqt/trimming_paired.nf
index f15efac0c306cd09280b791035fccfc3efc6f039..0b28219c1db247aba868beea8e472abe14629d39 100644
--- a/src/nf_modules/urqt/trimming_paired.nf
+++ b/src/nf_modules/urqt/trimming_paired.nf
@@ -8,6 +8,7 @@ Channel
process trimming {
tag "${reads}"
publishDir "results/fastq/trimming/", mode: 'copy'
+ label "urqt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 374112e5218fa5916800f3c92bd6f989d59a9aa2..e1843f172a39b7bd0013eb2c0dc7a6cc831d90f7 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_single.nf b/src/nf_modules/urqt/trimming_single.nf
index 4116a69a7af5164ea59aa918fd314238f5068b77..42bc7c2c5dc6cc4444ba519e9b94a397bcf6af22 100644
--- a/src/nf_modules/urqt/trimming_single.nf
+++ b/src/nf_modules/urqt/trimming_single.nf
@@ -11,6 +11,7 @@ Channel
process trimming {
tag "$file_id"
echo true
+ label "urqt"
input:
set file_id, file(reads) from fastq_files