From 11a52fbcd95757625f8140c2d3694f6ed0f98f3d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 17:05:45 +0100
Subject: [PATCH] Bowtie: add singularity to nf files
---
src/nf_modules/Bowtie/indexing.config | 14 +++++++++++++-
src/nf_modules/Bowtie/indexing.nf | 1 -
src/nf_modules/Bowtie/mapping_paired.config | 11 +++++++++++
src/nf_modules/Bowtie/mapping_paired.nf | 1 -
src/nf_modules/Bowtie/mapping_single.config | 11 +++++++++++
src/nf_modules/Bowtie/mapping_single.nf | 1 -
src/nf_modules/Bowtie/tests.sh | 18 ++++++++++++++++++
7 files changed, 53 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index 954b245..5e9d823 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -4,10 +4,20 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
+ cpus = 4
container = "bowtie:1.2.2"
}
}
}
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: index_fasta {
+ cpus = 4
+ container = "file://bin/bowtie:1.2.2.sif"
+ }
+ }
+ }
psmn {
process{
withName: index_fasta {
@@ -16,8 +26,10 @@ profiles {
executor = "sge"
clusterOptions = "-m e -cwd -V"
memory = "20GB"
+ cpus = 16
time = "12h"
- queue = 'monointeldeb128'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
}
}
diff --git a/src/nf_modules/Bowtie/indexing.nf b/src/nf_modules/Bowtie/indexing.nf
index 537d684..cf6bfae 100644
--- a/src/nf_modules/Bowtie/indexing.nf
+++ b/src/nf_modules/Bowtie/indexing.nf
@@ -11,7 +11,6 @@ Channel
process index_fasta {
tag "$fasta.baseName"
- cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index 5b3b9f9..b27917e 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: mapping_fastq {
container = "bowtie:1.2.2"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "file://bin/bowtie:1.2.2.sif"
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie/mapping_paired.nf b/src/nf_modules/Bowtie/mapping_paired.nf
index cc9f40b..e92cb3d 100644
--- a/src/nf_modules/Bowtie/mapping_paired.nf
+++ b/src/nf_modules/Bowtie/mapping_paired.nf
@@ -19,7 +19,6 @@ Channel
process mapping_fastq {
tag "$pair_id"
- cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index 5b3b9f9..b27917e 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: mapping_fastq {
container = "bowtie:1.2.2"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "file://bin/bowtie:1.2.2.sif"
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "Bowtie/1.2.2:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie/mapping_single.nf b/src/nf_modules/Bowtie/mapping_single.nf
index ad9754d..490cb1d 100644
--- a/src/nf_modules/Bowtie/mapping_single.nf
+++ b/src/nf_modules/Bowtie/mapping_single.nf
@@ -19,7 +19,6 @@ Channel
process mapping_fastq {
tag "$file_id"
- cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie/tests.sh b/src/nf_modules/Bowtie/tests.sh
index 803f628..3df87df 100755
--- a/src/nf_modules/Bowtie/tests.sh
+++ b/src/nf_modules/Bowtie/tests.sh
@@ -15,3 +15,21 @@
--index "results/mapping/index/*.ebwt" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/Bowtie/indexing.nf \
+ -c src/nf_modules/Bowtie/indexing.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+
+./nextflow src/nf_modules/Bowtie/mapping_single.nf \
+ -c src/nf_modules/Bowtie/mapping_single.config \
+ -profile singularity \
+ --index "results/mapping/index/*.ebwt" \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
+ -c src/nf_modules/Bowtie/mapping_paired.config \
+ -profile singularity \
+ --index "results/mapping/index/*.ebwt" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+fi
--
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