From 786e69deedfc98d6623e35ac8ffcc7d0e5655ef0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Jun 2018 16:41:52 +0200
Subject: [PATCH] Bowtie2: add nf files and tests

---
 src/nf_modules/Bowtie2/bowtie2.config         |  24 ++++
 src/nf_modules/Bowtie2/bowtie2.nf             | 125 ++++++++++++++++++
 src/nf_modules/Bowtie2/tests/index.nf         |  31 +++++
 .../Bowtie2/tests/mapping_paired.nf           |  39 ++++++
 .../Bowtie2/tests/mapping_single.nf           |  38 ++++++
 src/nf_modules/Bowtie2/tests/tests.sh         |  17 +++
 6 files changed, 274 insertions(+)
 create mode 100644 src/nf_modules/Bowtie2/bowtie2.config
 create mode 100644 src/nf_modules/Bowtie2/bowtie2.nf
 create mode 100644 src/nf_modules/Bowtie2/tests/index.nf
 create mode 100644 src/nf_modules/Bowtie2/tests/mapping_paired.nf
 create mode 100644 src/nf_modules/Bowtie2/tests/mapping_single.nf
 create mode 100644 src/nf_modules/Bowtie2/tests/tests.sh

diff --git a/src/nf_modules/Bowtie2/bowtie2.config b/src/nf_modules/Bowtie2/bowtie2.config
new file mode 100644
index 0000000..18ffbc6
--- /dev/null
+++ b/src/nf_modules/Bowtie2/bowtie2.config
@@ -0,0 +1,24 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $index_fasta {
+        container = "bowtie2:2.3.4.1"
+      }
+      $mapping_fastq {
+        container = "bowtie2:2.3.4.1"
+      }
+    }
+  }
+  sge {
+    process{
+      $index_fasta {
+        beforeScript = "module purge; module load Bowite2/2.3.4.1"
+      }
+      $mapping_fastq {
+        beforeScript = "module purge; module load SAMtools/1.7; module load Bowite2/2.3.4.1"
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
new file mode 100644
index 0000000..fe19db8
--- /dev/null
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -0,0 +1,125 @@
+/*
+* Bowtie2 :
+* Imputs : fastq files
+* Imputs : fasta files
+* Output : bam files
+*/
+
+/*                      fasta indexing                                     */
+params.fasta = "$baseDir/data/bam/*.fasta"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .set { fasta_file }
+
+process index_fasta {
+  tag "$fasta.baseName"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_file
+
+  output:
+    file "*.index*" into index_files
+
+  script:
+"""
+bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.index = "$baseDir/data/index/*.index.*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$pair_id"
+  cpus 4
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+  file index from index_files.collect()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+"""
+ bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
+ -1 ${reads[0]} -2 ${reads[1]} 2> \
+ ${pair_id}_bowtie2_report.txt | \
+ samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$reads.baseName"
+  cpus 4
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  file reads from fastq_files
+  file index from index_files.collect()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+"""
+bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
+-U ${reads} 2> \
+${reads.baseName}_bowtie2_report.txt | \
+samtools view -Sb - > ${reads.baseName}.bam
+
+if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
diff --git a/src/nf_modules/Bowtie2/tests/index.nf b/src/nf_modules/Bowtie2/tests/index.nf
new file mode 100644
index 0000000..2636f4b
--- /dev/null
+++ b/src/nf_modules/Bowtie2/tests/index.nf
@@ -0,0 +1,31 @@
+params.fasta = "$baseDir/data/bam/*.fasta"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .set { fasta_file }
+
+process index_fasta {
+  tag "$fasta.baseName"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_file
+
+  output:
+    file "*.index*" into index_files
+
+  script:
+"""
+bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
new file mode 100644
index 0000000..c6c79b8
--- /dev/null
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -0,0 +1,39 @@
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.index = "$baseDir/data/index/*.index.*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$pair_id"
+  cpus 4
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+  file index from index_files.collect()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+"""
+ bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
+ -1 ${reads[0]} -2 ${reads[1]} 2> \
+ ${pair_id}_bowtie2_report.txt | \
+ samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
new file mode 100644
index 0000000..70c55b7
--- /dev/null
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -0,0 +1,38 @@
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$reads.baseName"
+  cpus 4
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  file reads from fastq_files
+  file index from index_files.collect()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+"""
+bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
+-U ${reads} 2> \
+${reads.baseName}_bowtie2_report.txt | \
+samtools view -Sb - > ${reads.baseName}.bam
+
+if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
diff --git a/src/nf_modules/Bowtie2/tests/tests.sh b/src/nf_modules/Bowtie2/tests/tests.sh
new file mode 100644
index 0000000..888e698
--- /dev/null
+++ b/src/nf_modules/Bowtie2/tests/tests.sh
@@ -0,0 +1,17 @@
+nextflow src/nf_modules/Bowtie2/tests/index.nf \
+  -c src/nf_modules/Bowtie2/bowtie2.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+
+nextflow src/nf_modules/Bowtie2/tests/mapping_single.nf \
+  -c src/nf_modules/Bowtie2/bowtie2.config \
+  -profile docker \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
+
+nextflow src/nf_modules/Bowtie2/tests/mapping_paired.nf \
+  -c src/nf_modules/Bowtie2/bowtie2.config \
+  -profile docker \
+  --index "data/tiny_dataset/fasta/*.bt2" \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
-- 
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