From a2f71be3b60ea0d89e7e8672406ebe461a84dd61 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 18 Sep 2018 10:29:08 +0200
Subject: [PATCH] SNP_calling.nf: QC and mapping
---
src/SNP_calling.nf | 94 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 94 insertions(+)
create mode 100644 src/SNP_calling.nf
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
new file mode 100644
index 0000000..248890f
--- /dev/null
+++ b/src/SNP_calling.nf
@@ -0,0 +1,94 @@
+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
+"""
+}
+
--
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