From cbd23ab657eb28ecb515824d97fadf5144eed196 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 17:19:09 +0100
Subject: [PATCH] Bowtie2: add singularity to nf files
---
src/nf_modules/Bowtie2/indexing.config | 18 +++++++++--
src/nf_modules/Bowtie2/indexing.nf | 1 -
src/nf_modules/Bowtie2/mapping_paired.config | 11 +++++++
src/nf_modules/Bowtie2/mapping_paired.nf | 1 -
src/nf_modules/Bowtie2/mapping_single.config | 11 +++++++
src/nf_modules/Bowtie2/mapping_single.nf | 1 -
src/nf_modules/Bowtie2/tests.sh | 30 +++++++++++++++++--
.../Bowtie2/2.3.4.1/Bowtie2.def | 23 ++++++++++++++
.../Bowtie2/2.3.4.1/build.sh | 3 ++
9 files changed, 90 insertions(+), 9 deletions(-)
create mode 100644 src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
create mode 100755 src/singularity_modules/Bowtie2/2.3.4.1/build.sh
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 434889bc..c53d855a 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -3,21 +3,33 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withName: mapping_fastq {
+ withName: index_fasta {
container = "bowtie2:2.3.4.1"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: index_fasta {
+ container = "file://bin/bowtie2:2.3.4.1.sif"
+ cpus = 4
}
}
}
psmn {
process{
- withName: mapping_fastq {
+ withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "20GB"
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/Bowtie2/indexing.nf b/src/nf_modules/Bowtie2/indexing.nf
index 4f3cde5e..45318049 100644
--- a/src/nf_modules/Bowtie2/indexing.nf
+++ b/src/nf_modules/Bowtie2/indexing.nf
@@ -9,7 +9,6 @@ Channel
process index_fasta {
tag "$fasta.baseName"
- cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 30150ff9..27933c3b 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: mapping_fastq {
container = "bowtie2:2.3.4.1"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ container = "file://bin/bowtie2:2.3.4.1.sif"
+ cpus = 4
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/Bowtie2/mapping_paired.nf b/src/nf_modules/Bowtie2/mapping_paired.nf
index 7422b143..dc466740 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/mapping_paired.nf
@@ -15,7 +15,6 @@ Channel
process mapping_fastq {
tag "$pair_id"
- cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 30150ff9..27933c3b 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: mapping_fastq {
container = "bowtie2:2.3.4.1"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ container = "file://bin/bowtie2:2.3.4.1.sif"
+ cpus = 4
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "Bowtie2/2.3.4.1: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/Bowtie2/mapping_single.nf b/src/nf_modules/Bowtie2/mapping_single.nf
index 66676991..1b7954ec 100644
--- a/src/nf_modules/Bowtie2/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/mapping_single.nf
@@ -15,7 +15,6 @@ Channel
process mapping_fastq {
tag "$file_id"
- cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
diff --git a/src/nf_modules/Bowtie2/tests.sh b/src/nf_modules/Bowtie2/tests.sh
index ab148382..01e349a7 100755
--- a/src/nf_modules/Bowtie2/tests.sh
+++ b/src/nf_modules/Bowtie2/tests.sh
@@ -1,17 +1,41 @@
./nextflow src/nf_modules/Bowtie2/indexing.nf \
-c src/nf_modules/Bowtie2/indexing.config \
-profile docker \
- --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
-c src/nf_modules/Bowtie2/mapping_single.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
-c src/nf_modules/Bowtie2/mapping_paired.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
- --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/Bowtie2/indexing.nf \
+ -c src/nf_modules/Bowtie2/indexing.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
+
+./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
+ -c src/nf_modules/Bowtie2/mapping_single.config \
+ -profile singularity \
+ --index "data/tiny_dataset/fasta/*.bt2" \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+ -resume
+
+./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
+ -c src/nf_modules/Bowtie2/mapping_paired.config \
+ -profile singularity \
+ --index "data/tiny_dataset/fasta/*.bt2" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
+fi
diff --git a/src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def b/src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
new file mode 100644
index 00000000..73a177e4
--- /dev/null
+++ b/src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
@@ -0,0 +1,23 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BOWTIE2_VERSION=2.3.4.1
+SAMTOOLS_VERSION=1.7
+PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
+samtools=${SAMTOOLS_VERSION}* \
+perl=5.26.1*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+%environment
+export BOWTIE2_VERSION=2.3.4.1
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/Bowtie2/2.3.4.1/build.sh b/src/singularity_modules/Bowtie2/2.3.4.1/build.sh
new file mode 100755
index 00000000..398fb1c7
--- /dev/null
+++ b/src/singularity_modules/Bowtie2/2.3.4.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
+singularity sign bin/bowtie2:2.3.4.1.sif
--
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