src/SNP_calling.nf: add Mutect2 to call SNP

src/SNP_calling.nf

 params.fastq = "$baseDir/data/*.fastq"
 params.fasta = "$baseDir/data/*.fasta"
+params.sam = ""
 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}" }
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
   .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fasta_file }
+  .into { fasta_file;
+     indel_fasta_file;
+     recalibration_fasta_file;
+     haplotypecaller_fasta_file
+  }
 Channel
   .fromFilePairs( params.fastq )
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
   .set { fastq_files }
 
-process adaptor_removal {
-  tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+if (params.sam == "") {
+  process adaptor_removal {
+    tag "$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
+  """
+  }
+} else {
+  Channel
+    .fromPath( params.sam )
+    .ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
+    .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+    .set { sam_files }
+}
+
+process dedup_sam {
+  tag "$file_id"
+  cpus 4
 
   input:
-  set pair_id, file(reads) from fastq_files
+    set file_id, file(sam) from sam_files
 
   output:
-  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
-
+    set file_id, "*_dedup.sam*" into dedup_sam_files
   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
+samblaster --addMateTags -i ${sam} -o ${file_id}_dedup.sam
 """
 }
 
-process trimming {
-  tag "${reads}"
+process sort_bam {
+  tag "$file_id"
   cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
+  publishDir "results/mapping/bam/1_dedup/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files_cut
+    set file_id, file(sam) from dedup_sam_files
 
   output:
-  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+    set file_id, "*_sorted.bam" into sorted_bam_files
 
   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
+sambamba view -t ${task.cpus} -S -f bam -l 0 ${sam} | \
+sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam /dev/stdin
 """
 }
 
-process index_fasta {
-  tag "$fasta_id"
+sorted_bam_files.into{
+  index_sorted_bam_files;
+  haplotypecaller_sorted_bam_files
+}
+
+process index_bam {
+  tag "$file_id"
   cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
+  publishDir "results/mapping/bam/2_realigned/", mode: 'copy'
 
   input:
-    set fasta_id, file(fasta) from fasta_file
+    set file_id, file(bam) from index_sorted_bam_files
 
   output:
-    set fasta_id, "${fasta.baseName}.*" into index_files
-    file "*_bwa_report.txt" into index_files_report
+    set file_id, "*.bam*" into indexed_bam_files
 
   script:
 """
-bwa index -p ${fasta.baseName} ${fasta} \
-&> ${fasta.baseName}_bwa_report.txt
+sambamba index -t ${task.cpus} ${bam}
 """
 }
 
+haplotypecaller_fasta_file.into{
+    haplo_fasta_file;
+    index2_fasta_file
+    index3_fasta_file
+  }
+
+process index2_fasta {
+  tag "$file_id"
+  publishDir "results/mapping/bam/2_realigned/", mode: 'copy'
 
-process mapping_fastq {
-  tag "$reads"
+  input:
+    set genome_id, file(fasta) from index2_fasta_file
+
+  output:
+    set genome_id, "*.dict" into indexed2_fasta_file
+
+  script:
+"""
+gatk CreateSequenceDictionary -R ${fasta} &> gatk_output.txt
+"""
+}
+
+process index3_fasta {
+  tag "$file_id"
+  publishDir "results/mapping/bam/2_realigned/", mode: 'copy'
+
+  input:
+    set genome_id, file(fasta) from index3_fasta_file
+
+  output:
+    set genome_id, "*.fai" into indexed3_fasta_file
+
+  script:
+"""
+samtools faidx ${fasta}
+"""
+}
+
+process HaplotypeCaller {
+  tag "$file_id"
   cpus 4
-  publishDir "results/mapping/sam/", mode: 'copy'
+  publishDir "results/SNP/vcf/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files_trim
-  set index_id, file(index) from index_files.collect()
+    set file_id, file(bam) from haplotypecaller_sorted_bam_files.collect()
+    set file_ididx, file(bamidx) from indexed_bam_files.collect()
+    set genome_id, file(fasta) from haplo_fasta_file.collect()
+    set genome2_idx, file(fasta2idx) from indexed2_fasta_file.collect()
+    set genome3_idx, file(fasta3idx) from indexed3_fasta_file.collect()
 
   output:
-  file "${pair_id}.sam" into sam_files
-  file "${pair_id}_bwa_report.txt" into mapping_repport_files
+    set file_id, "*.vcf" into vcf_files
+    set file_id, "*.bam" into realigned_bams_files
 
   script:
 """
-bwa mem -t ${task.cpus} \
-${index_id} ${reads[0]} ${reads[1]} \
--o ${pair_id}.sam &> ${pair_id}_bwa_report.txt
+gatk Mutect2 --native-pair-hmm-threads ${task.cpus} -R ${fasta} \
+-I ${bam} -tumor ${params.tumor} -normal ${params.normal} \
+-O ${file_id}_raw_calls.g.vcf \
+-bamout ${file_id}_realigned.bam
 """
 }
 
+