From f92cde7ca41e42c35673f28ce54a8b551a7bd4d9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 7 Jun 2019 11:05:07 +0200
Subject: [PATCH] subread nf: add nf config and test files
---
src/nf_modules/htseq/tests.sh | 2 +-
src/nf_modules/subread/subread.config | 109 ++++++++++++++++++++++++++
src/nf_modules/subread/subread.nf | 52 ++++++++++++
src/nf_modules/subread/tests.sh | 15 ++++
4 files changed, 177 insertions(+), 1 deletion(-)
create mode 100644 src/nf_modules/subread/subread.config
create mode 100644 src/nf_modules/subread/subread.nf
create mode 100755 src/nf_modules/subread/tests.sh
diff --git a/src/nf_modules/htseq/tests.sh b/src/nf_modules/htseq/tests.sh
index 904b42b3..eada26b6 100755
--- a/src/nf_modules/htseq/tests.sh
+++ b/src/nf_modules/htseq/tests.sh
@@ -8,7 +8,7 @@
if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/htseq/htseq.nf \
-c src/nf_modules/htseq/htseq.config \
- -profile docker \
+ -profile singularity \
--gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam" \
-resume
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
new file mode 100644
index 00000000..19f20463
--- /dev/null
+++ b/src/nf_modules/subread/subread.config
@@ -0,0 +1,109 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: sort_bam {
+ container = "samtools:1.7"
+ cpus = 1
+ }
+ withName: counting {
+ container = "subread:1.6.4"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: sort_bam {
+ container = "file://bin/samtools:1.7.img"
+ cpus = 1
+ }
+ withName: counting {
+ container = "file://bin/subread:1.6.4.img"
+ cpus = 1
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: sort_bam {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "samtools/1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ }
+ withName: counting {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "subread/1.6.4"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ }
+ }
+ }
+ ccin2p3_conda {
+ process{
+ withName: sort_bam {
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: counting {
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/subread_1.6.4"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: counting {
+ container = "/sps/lbmc/common/singularity/subread:1.6.4.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/subread/subread.nf b/src/nf_modules/subread/subread.nf
new file mode 100644
index 00000000..f0b53e39
--- /dev/null
+++ b/src/nf_modules/subread/subread.nf
@@ -0,0 +1,52 @@
+params.bam = "$baseDir/data/bam/*.bam"
+params.gtf = "$baseDir/data/annotation/*.gtf"
+
+log.info "bam files : ${params.bam}"
+log.info "gtf files : ${params.gtf}"
+
+Channel
+ .fromPath( params.bam )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bam_files }
+Channel
+ .fromPath( params.gtf )
+ .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
+ .set { gtf_file }
+
+process sort_bam {
+ tag "$file_id"
+ cpus 4
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ set file_id, "*_sorted.sam" into sorted_bam_files
+
+ script:
+"""
+# sort bam by name
+samtools sort -@ ${task.cpus} -n -O SAM -o ${file_id}_sorted.sam ${bam}
+"""
+}
+
+process counting {
+ tag "$file_id"
+ publishDir "results/quantification/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from sorted_bam_files
+ file gtf from gtf_file
+
+ output:
+ file "*.count" into count_files
+
+ script:
+"""
+featureCounts ${bam} -a ${gtf} -p \
+ -o ${file_id}.count \
+ -R BAM
+"""
+}
+
diff --git a/src/nf_modules/subread/tests.sh b/src/nf_modules/subread/tests.sh
new file mode 100755
index 00000000..c50b20e3
--- /dev/null
+++ b/src/nf_modules/subread/tests.sh
@@ -0,0 +1,15 @@
+./nextflow src/nf_modules/subread/subread.nf \
+ -c src/nf_modules/subread/subread.config \
+ -profile docker \
+ --gtf "data/tiny_dataset/annot/tiny.gff" \
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/subread/subread.nf \
+ -c src/nf_modules/subread/subread.config \
+ -profile singularity \
+ --gtf "data/tiny_dataset/annot/tiny.gff" \
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ -resume
+fi
--
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