From a494361b7ffe299e1ca0132188dd02e72f69c3f6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 16:06:39 +0100
Subject: [PATCH] BWA: add singularity to nf files
---
src/nf_modules/BWA/indexing.config | 16 ++++++++++--
src/nf_modules/BWA/indexing.nf | 1 -
src/nf_modules/BWA/mapping_paired.config | 11 ++++++++
src/nf_modules/BWA/mapping_paired.nf | 1 -
src/nf_modules/BWA/tests.sh | 29 +++++++++++++++++++--
src/singularity_modules/BWA/0.7.17/build.sh | 2 ++
6 files changed, 54 insertions(+), 6 deletions(-)
create mode 100755 src/singularity_modules/BWA/0.7.17/build.sh
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 2936204f..367e0dfd 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: index_fasta {
container = "bwa:0.7.17"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: index_fasta {
+ container = "file://bin/bwa:0.7.17.sif"
+ cpus = 4
}
}
}
@@ -15,9 +25,11 @@ profiles {
module = "BWA/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
- time = "12h"
- queue = 'monointeldeb128'
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
}
}
diff --git a/src/nf_modules/BWA/indexing.nf b/src/nf_modules/BWA/indexing.nf
index 67ea3287..09096eea 100644
--- a/src/nf_modules/BWA/indexing.nf
+++ b/src/nf_modules/BWA/indexing.nf
@@ -10,7 +10,6 @@ Channel
process index_fasta {
tag "$fasta_id"
- cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index ce8f7f45..5535fd10 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: mapping_fastq {
container = "bwa:0.7.17"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ container = "file://bin/bwa:0.7.17.sif"
+ cpus = 4
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "BWA/0.7.17"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/BWA/mapping_paired.nf b/src/nf_modules/BWA/mapping_paired.nf
index 5ac50ef5..7309c605 100644
--- a/src/nf_modules/BWA/mapping_paired.nf
+++ b/src/nf_modules/BWA/mapping_paired.nf
@@ -17,7 +17,6 @@ Channel
process mapping_fastq {
tag "$reads"
- cpus 4
publishDir "results/mapping/sam/", mode: 'copy'
input:
diff --git a/src/nf_modules/BWA/tests.sh b/src/nf_modules/BWA/tests.sh
index 1f3150cf..8f3c52da 100755
--- a/src/nf_modules/BWA/tests.sh
+++ b/src/nf_modules/BWA/tests.sh
@@ -1,7 +1,8 @@
./nextflow src/nf_modules/BWA/indexing.nf \
-c src/nf_modules/BWA/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/BWA/mapping_single.nf \
# -c src/nf_modules/BWA/mapping_single.config \
@@ -13,5 +14,29 @@
-c src/nf_modules/BWA/mapping_paired.config \
-profile docker \
--index "results/mapping/index/tiny_v2*" \
- --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/BWA/indexing.nf \
+ -c src/nf_modules/BWA/indexing.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ -resume
+
+
+# ./nextflow src/nf_modules/BWA/mapping_single.nf \
+# -c src/nf_modules/BWA/mapping_single.config \
+# -profile singularity \
+# --index "results/mapping/index/tiny_v2.index" \
+# --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+./nextflow src/nf_modules/BWA/mapping_paired.nf \
+ -c src/nf_modules/BWA/mapping_paired.config \
+ -profile singularity \
+ --index "results/mapping/index/tiny_v2*" \
+ --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+ -resume
+
+fi
diff --git a/src/singularity_modules/BWA/0.7.17/build.sh b/src/singularity_modules/BWA/0.7.17/build.sh
new file mode 100755
index 00000000..340a8c21
--- /dev/null
+++ b/src/singularity_modules/BWA/0.7.17/build.sh
@@ -0,0 +1,2 @@
+#/bin/sh
+sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/BWA/0.7.17/BWA.def
--
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