From dde8e8a29c59a80a67443db3db42ee3b8e30fdd2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Mar 2019 16:18:26 +0100
Subject: [PATCH] deeptools: add singularity to files
---
src/nf_modules/deeptools/bam_to_bigwig.config | 17 ++++++++++++++
src/nf_modules/deeptools/bam_to_bigwig.nf | 3 +--
.../deeptools/compute_matrix.config | 11 ++++++++++
src/nf_modules/deeptools/compute_matrix.nf | 1 -
src/nf_modules/deeptools/plot_profile.config | 11 ++++++++++
src/nf_modules/deeptools/plot_profile.nf | 1 -
src/nf_modules/deeptools/tests.sh | 22 +++++++++++++++++++
7 files changed, 62 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index ab28edcb..c3edbc6f 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -5,9 +5,24 @@ profiles {
process {
withName: index_bam {
container = "sambamba:0.6.7"
+ cpus = 4
}
withName: bam_to_bigwig {
container = "deeptools:3.0.2"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: index_bam {
+ container = "file://bin/sambamba:0.6.7.sif"
+ cpus = 4
+ }
+ withName: bam_to_bigwig {
+ container = "file://bin/deeptools:3.0.2.sif"
+ cpus = 4
}
}
}
@@ -18,6 +33,7 @@ profiles {
module = "sambamba/0.6.7"
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'
@@ -28,6 +44,7 @@ profiles {
module = "deeptools/3.0.2"
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/deeptools/bam_to_bigwig.nf b/src/nf_modules/deeptools/bam_to_bigwig.nf
index 85fa7870..4c30ee0e 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.nf
+++ b/src/nf_modules/deeptools/bam_to_bigwig.nf
@@ -15,7 +15,6 @@ bam_files.into{
process index_bam {
tag "$file_id"
- cpus 4
input:
set file_id, file(bam) from bam_files_index
@@ -33,7 +32,7 @@ bam_files_indexed = bam_files_bigwig.join(indexed_bam_file, by: 0)
process bam_to_bigwig {
tag "$file_id"
- cpus 4
+
publishDir "results/mapping/bigwig/", mode: 'copy'
input:
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 7159cbc7..c2c64bf4 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: compute_matrix {
container = "deeptools:3.0.2"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: compute_matrix {
+ container = "file://bin/deeptools:3.0.2.sif"
+ cpus = 4
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "deeptools/3.0.2"
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/deeptools/compute_matrix.nf b/src/nf_modules/deeptools/compute_matrix.nf
index d1d0ae07..2b6e0e91 100644
--- a/src/nf_modules/deeptools/compute_matrix.nf
+++ b/src/nf_modules/deeptools/compute_matrix.nf
@@ -17,7 +17,6 @@ Channel
process compute_matrix {
tag "$bed_file_id"
- cpus 4
publishDir "results/mapping/region_matrix/", mode: 'copy'
input:
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 984575cc..11626d8b 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: plot_profile {
container = "deeptools:3.0.2"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: compute_matrix {
+ container = "file://bin/deeptools:3.0.2.sif"
+ cpus = 4
}
}
}
@@ -15,6 +25,7 @@ profiles {
module = "deeptools/3.0.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
+ cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/deeptools/plot_profile.nf b/src/nf_modules/deeptools/plot_profile.nf
index eb089714..dfce4e55 100644
--- a/src/nf_modules/deeptools/plot_profile.nf
+++ b/src/nf_modules/deeptools/plot_profile.nf
@@ -12,7 +12,6 @@ Channel
process plot_profile {
tag "$file_id"
- cpus 4
publishDir "results/mapping/region_matrix/", mode: 'copy'
input:
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
index 8c95d405..4253689a 100755
--- a/src/nf_modules/deeptools/tests.sh
+++ b/src/nf_modules/deeptools/tests.sh
@@ -22,3 +22,25 @@ cp data/tiny_dataset/map/tiny_v2.sort.bam \
--matrix "results/mapping/region_matrix/*.mat.gz" \
--title "plot title" \
-resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+ -c src/nf_modules/deeptools/bam_to_bigwig.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+ -resume
+
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+ -c src/nf_modules/deeptools/compute_matrix.config \
+ -profile docker \
+ --bw "results/mapping/bigwig/*.bw" \
+ --bed "data/tiny_dataset/annot/tiny.bed" \
+ -resume
+
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+ -c src/nf_modules/deeptools/plot_profile.config \
+ -profile docker \
+ --matrix "results/mapping/region_matrix/*.mat.gz" \
+ --title "plot title" \
+ -resume
+fi
--
GitLab