SNP_calling.nf: QC and mapping

src/SNP_calling.nf

+params.fastq = "$baseDir/data/*.fastq"
+params.fasta = "$baseDir/data/*.fasta"
+log.info "fastq files : ${params.fastq}"
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { fasta_file }
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$pair_id"
+  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+  script:
+"""
+cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+"""
+}
+
+process trimming {
+  tag "${reads}"
+  cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_cut
+
+  output:
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+
+  script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+--in ${reads[0]} --inpair ${reads[1]} \
+--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+process index_fasta {
+  tag "$fasta_id"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    set fasta_id, file(fasta) from fasta_file
+
+  output:
+    set fasta_id, "${fasta.baseName}.*" into index_files
+    file "*_bwa_report.txt" into index_files_report
+
+  script:
+"""
+bwa index -p ${fasta.baseName} ${fasta} \
+&> ${fasta.baseName}_bwa_report.txt
+"""
+}
+
+
+process mapping_fastq {
+  tag "$reads"
+  cpus 4
+  publishDir "results/mapping/sam/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_trim
+  set index_id, file(index) from index_files.collect()
+
+  output:
+  file "${pair_id}.sam" into sam_files
+  file "${pair_id}_bwa_report.txt" into mapping_repport_files
+
+  script:
+"""
+bwa mem -t ${task.cpus} \
+${index_id} ${reads[0]} ${reads[1]} \
+-o ${pair_id}.sam &> ${pair_id}_bwa_report.txt
+"""
+}
+