Bowtie: add nf files

src/nf_modules/Bowtie/bowtie.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $index_fasta {
+        container = "bowtie:1.2.2"
+      }
+      $mapping_fastq {
+        container = "bowtie:1.2.2"
+      }
+    }
+  }
+  sge {
+    process{
+      $index_fasta {
+        beforeScript = "module purge; module load Bowtie/1.2.2"
+      }
+      $mapping_fastq {
+        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
+      }
+    }
+  }
+}

src/nf_modules/Bowtie/bowtie.nf

+/*
+* Bowtie :
+* 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:
+"""
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$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.toList()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.ebwt/) {
+        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+    }
+  }
+"""
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-1 ${reads[0]} -2 ${reads[1]} 2> \
+${pair_id}_bowtie_report.txt | \
+samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
+/*
+* for single-end data
+*/
+params.fastq = "$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.toList()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+index_id = index[0]
+for (index_file in index) {
+  if (index_file =~ /.*\.1\.ebwt/) {
+      index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+  }
+}
+"""
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-U ${reads} 2> \
+${reads.baseName}_bowtie_report.txt | \
+samtools view -Sb - > ${reads.baseName}.bam
+
+if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}

src/nf_modules/Bowtie/tests/index.nf

+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:
+"""
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}
+

src/nf_modules/Bowtie/tests/mapping_paired.nf

+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.toList()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.ebwt/) {
+        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+    }
+  }
+"""
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-1 ${reads[0]} -2 ${reads[1]} 2> \
+${pair_id}_bowtie_report.txt | \
+samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}
+
+

src/nf_modules/Bowtie/tests/mapping_single.nf

+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.toList()
+
+  output:
+  file "*.bam" into bam_files
+
+  script:
+index_id = index[0]
+for (index_file in index) {
+  if (index_file =~ /.*\.1\.ebwt/) {
+      index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+  }
+}
+"""
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-U ${reads} 2> \
+${reads.baseName}_bowtie_report.txt | \
+samtools view -Sb - > ${reads.baseName}.bam
+
+if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}

src/nf_modules/Bowtie/tests/tests.sh

+./nextflow src/nf_modules/Bowtie/tests/index.nf \
+  -c src/nf_modules/Bowtie/bowtie.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+
+./nextflow src/nf_modules/Bowtie/tests/mapping_single.nf \
+  -c src/nf_modules/Bowtie/bowtie.config \
+  -profile docker \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+./nextflow src/nf_modules/Bowtie/tests/mapping_paired.nf \
+  -c src/nf_modules/Bowtie/bowtie.config \
+  -profile docker \
+  --index "results/mapping/index/*.ebwt" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
+