From 58d2e60a79a3bec18a771c8031ab98967afedf59 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 29 Mar 2019 11:02:01 +0100
Subject: [PATCH] hisat2: update process and config to match new format
---
.../hisat2/{test => }/bam_converter.nf | 0
src/nf_modules/hisat2/indexing.config | 36 +++++++++++++++++++
.../hisat2/{test/index.nf => indexing.nf} | 2 +-
src/nf_modules/hisat2/mapping_paired.config | 36 +++++++++++++++++++
.../hisat2/{test => }/mapping_paired.nf | 14 +++++---
src/nf_modules/hisat2/mapping_single.config | 36 +++++++++++++++++++
.../hisat2/{test => }/mapping_single.nf | 16 ++++++---
src/nf_modules/hisat2/{test => }/tests.sh | 0
8 files changed, 129 insertions(+), 11 deletions(-)
rename src/nf_modules/hisat2/{test => }/bam_converter.nf (100%)
create mode 100644 src/nf_modules/hisat2/indexing.config
rename src/nf_modules/hisat2/{test/index.nf => indexing.nf} (90%)
create mode 100644 src/nf_modules/hisat2/mapping_paired.config
rename src/nf_modules/hisat2/{test => }/mapping_paired.nf (65%)
create mode 100644 src/nf_modules/hisat2/mapping_single.config
rename src/nf_modules/hisat2/{test => }/mapping_single.nf (59%)
rename src/nf_modules/hisat2/{test => }/tests.sh (100%)
diff --git a/src/nf_modules/hisat2/test/bam_converter.nf b/src/nf_modules/hisat2/bam_converter.nf
similarity index 100%
rename from src/nf_modules/hisat2/test/bam_converter.nf
rename to src/nf_modules/hisat2/bam_converter.nf
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
new file mode 100644
index 00000000..dbbb4a2e
--- /dev/null
+++ b/src/nf_modules/hisat2/indexing.config
@@ -0,0 +1,36 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: index_fasta {
+ cpus = 4
+ container = "hisat2:2.0.0"
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: index_fasta {
+ cpus = 4
+ container = "file://bin/hisat2:2.0.0.sif"
+ }
+ }
+ }
+ sge {
+ process{
+ withName: index_fasta {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.0.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/hisat2/test/index.nf b/src/nf_modules/hisat2/indexing.nf
similarity index 90%
rename from src/nf_modules/hisat2/test/index.nf
rename to src/nf_modules/hisat2/indexing.nf
index 7b30f7db..563a13c2 100644
--- a/src/nf_modules/hisat2/test/index.nf
+++ b/src/nf_modules/hisat2/indexing.nf
@@ -27,6 +27,6 @@ process index_fasta {
script:
"""
-hisat2-build ${fasta} ${fasta.baseName}.index
+hisat2-build -p {task.cpus} ${fasta} ${fasta.baseName}.index
"""
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
new file mode 100644
index 00000000..6f3aa47b
--- /dev/null
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -0,0 +1,36 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "hisat2:2.0.0"
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "file://bin/hisat2:2.0.0.sif"
+ }
+ }
+ }
+ sge {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.0.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/hisat2/test/mapping_paired.nf b/src/nf_modules/hisat2/mapping_paired.nf
similarity index 65%
rename from src/nf_modules/hisat2/test/mapping_paired.nf
rename to src/nf_modules/hisat2/mapping_paired.nf
index 8350ebc0..d7bf9696 100644
--- a/src/nf_modules/hisat2/test/mapping_paired.nf
+++ b/src/nf_modules/hisat2/mapping_paired.nf
@@ -14,20 +14,24 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads"
- //tag "$index.baseName"
- cpus 4
+ tag "$pair_id"
publishDir "results/mapping/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
- file index from index_files.toList()
+ file index from index_files.collect()
output:
file "*" into counts_files
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
-hisat2 -x ${file(file(index[0]).baseName).baseName} -1 ${reads[0]} -2 ${reads[1]} -S ${pair_id}.sam -p ${task.cpus}
+hisat2 -x ${index_id} -1 ${reads[0]} -2 ${reads[1]} -S ${pair_id}.sam -p ${task.cpus}
"""
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
new file mode 100644
index 00000000..6f3aa47b
--- /dev/null
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -0,0 +1,36 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "hisat2:2.0.0"
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: mapping_fastq {
+ cpus = 4
+ container = "file://bin/hisat2:2.0.0.sif"
+ }
+ }
+ }
+ sge {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.0.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/hisat2/test/mapping_single.nf b/src/nf_modules/hisat2/mapping_single.nf
similarity index 59%
rename from src/nf_modules/hisat2/test/mapping_single.nf
rename to src/nf_modules/hisat2/mapping_single.nf
index f6740b72..93506140 100644
--- a/src/nf_modules/hisat2/test/mapping_single.nf
+++ b/src/nf_modules/hisat2/mapping_single.nf
@@ -11,6 +11,7 @@ log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -18,19 +19,24 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
- cpus 4
+ tag "$file_id"
publishDir "results/mapping/", mode: 'copy'
input:
- file reads from fastq_files
- file index from index_files.toList()
+ set file_id, file(reads) from fastq_files
+ file index from index_files.collect()
output:
file "*" into count_files
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
-hisat2 -x ${file(file(index[0]).baseName).baseName} -U ${reads} -S ${reads.baseName}.sam -p ${task.cpus}
+hisat2 -x ${index_id} -U ${reads} -S ${file_id}.sam -p ${task.cpus}
"""
}
diff --git a/src/nf_modules/hisat2/test/tests.sh b/src/nf_modules/hisat2/tests.sh
similarity index 100%
rename from src/nf_modules/hisat2/test/tests.sh
rename to src/nf_modules/hisat2/tests.sh
--
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