From 5cdad1d72d16bc73b7b47da0a754f08f21e73b95 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 9 Oct 2020 12:07:02 +0200
Subject: [PATCH] nf_module update practical example to use withLabel instead
of withName
---
src/.docker_modules/kallistobustools/0.39.3/Dockerfile | 2 +-
src/nf_modules/bedtools/fasta_from_bed.config | 8 ++++----
src/nf_modules/bedtools/fasta_from_bed.nf | 1 +
src/nf_modules/bowtie/indexing.config | 8 ++++----
src/nf_modules/bowtie/indexing.nf | 1 +
src/nf_modules/bowtie/mapping_paired.config | 8 ++++----
src/nf_modules/bowtie/mapping_paired.nf | 1 +
src/nf_modules/bowtie/mapping_single.config | 8 ++++----
src/nf_modules/bowtie/mapping_single.nf | 1 +
src/nf_modules/bowtie2/indexing.config | 8 ++++----
src/nf_modules/bowtie2/indexing.nf | 1 +
src/nf_modules/bowtie2/mapping_paired.config | 8 ++++----
src/nf_modules/bowtie2/mapping_paired.nf | 1 +
src/nf_modules/bowtie2/mapping_single.config | 8 ++++----
src/nf_modules/bowtie2/mapping_single.nf | 1 +
src/nf_modules/cutadapt/adaptor_removal_paired.config | 8 ++++----
src/nf_modules/cutadapt/adaptor_removal_paired.nf | 1 +
src/nf_modules/cutadapt/adaptor_removal_single.config | 8 ++++----
src/nf_modules/cutadapt/adaptor_removal_single.nf | 1 +
src/nf_modules/cutadapt/trimming_paired.config | 8 ++++----
src/nf_modules/cutadapt/trimming_paired.nf | 1 +
src/nf_modules/cutadapt/trimming_single.config | 8 ++++----
src/nf_modules/cutadapt/trimming_single.nf | 1 +
src/nf_modules/kallisto/indexing.config | 8 ++++----
src/nf_modules/kallisto/indexing.nf | 1 +
src/nf_modules/kallisto/mapping_paired.config | 8 ++++----
src/nf_modules/kallisto/mapping_paired.nf | 1 +
src/nf_modules/kallisto/mapping_single.config | 8 ++++----
src/nf_modules/kallisto/mapping_single.nf | 1 +
src/nf_modules/urqt/trimming_paired.config | 8 ++++----
src/nf_modules/urqt/trimming_paired.nf | 1 +
src/nf_modules/urqt/trimming_single.config | 8 ++++----
src/nf_modules/urqt/trimming_single.nf | 1 +
33 files changed, 81 insertions(+), 65 deletions(-)
diff --git a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
index c993e745..1649aeed 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-${B_VERSION} && \
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index a04494e6..077270d7 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: fasta_from_bed {
+ withLabel: bedtools {
container = "lbmc/bedtools:2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$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 5e7504dc..85dce555 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 "${bed.baseName}"
publishDir "results/fasta/", mode: 'copy'
+ label "bedtools"
input:
file fasta from fasta_files
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index ccf47042..50dff965 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: index_fasta {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 cf6bfaee..d09a5de8 100644
--- a/src/nf_modules/bowtie/indexing.nf
+++ b/src/nf_modules/bowtie/indexing.nf
@@ -12,6 +12,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "bowtie"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index e6c7c6da..1d924e9b 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 90b47ba4..6357a8b6 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 "$pair_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index e6c7c6da..1d924e9b 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie {
cpus = 4
container = "lbmc/bowtie:1.2.2"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie {
container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 268bdfa8..ac287193 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 "$file_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 773c5eae..5a487f8e 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 45318049..e1ec9ae9 100644
--- a/src/nf_modules/bowtie2/indexing.nf
+++ b/src/nf_modules/bowtie2/indexing.nf
@@ -10,6 +10,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "bowtie2"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index b9f515f1..addc6b2e 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 225508d8..96c209fd 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 "$pair_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie2"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index b9f515f1..addc6b2e 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: bowtie2 {
container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 b5bfff2b..69db77e2 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 "$file_id"
publishDir "results/mapping/bams/", mode: 'copy'
+ label "bowtie2"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index ea069fd8..33b2179f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$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 f78d5c2d..0d203733 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 "$pair_id"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+ label "cutadapt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index ea069fd8..33b2179f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: adaptor_removal {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$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 26f3cd76..ac2b631e 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 "$file_id"
+ label "cutadapt"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index d69a7021..33b2179f 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$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 704240f4..9fb317ff 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 "$pair_id"
publishDir "results/fastq/trimming/", mode: 'copy'
+ label "cutadapt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index d69a7021..33b2179f 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: cutadapt {
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -40,7 +40,7 @@ profiles {
singularity.cacheDir = "$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 9b3764db..0d125e7e 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 "$file_id"
+ label "cutadapt"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 52d83cf2..1f3f39e8 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName index_fasta {
+ withLabel kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: index_fasta {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: index_fasta {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 ea153569..5b0fba5e 100644
--- a/src/nf_modules/kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -10,6 +10,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
+ label "kallisto"
input:
file fasta from fasta_file
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 839ae331..962e1fdc 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 455e70cd..56f13000 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 "$reads"
publishDir "results/mapping/quantification/", mode: 'copy'
+ label "kallisto"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 839ae331..962e1fdc 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: mapping_fastq {
+ withLabel: kallisto {
container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 95bed864..7ae21280 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 "$file_id"
publishDir "results/mapping/quantification/", mode: 'copy'
+ label "kallisto"
input:
set file_id, file(reads) from fastq_files
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index f5ca8084..f8f533f4 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: urqt {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: urqt {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 f15efac0..0b28219c 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 "${reads}"
publishDir "results/fastq/trimming/", mode: 'copy'
+ label "urqt"
input:
set pair_id, file(reads) from fastq_files
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 374112e5..e1843f17 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
cpus = 4
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
cpus = 4
}
@@ -24,7 +24,7 @@ profiles {
singularity.cacheDir = "/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
- withName: trimming {
+ withLabel: urqt {
container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
@@ -41,7 +41,7 @@ profiles {
singularity.cacheDir = "$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 4116a69a..42bc7c2c 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
--
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