src/nf_modules/Hisat2/hisat2.nf : process nextflow for running hisat2

src/nf_modules/Hisat2/hisat2.nf

+/*
+* Hisat2 :
+* 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 fasta files matching: ${params.fasta}" }
+  .set { fasta_file }
+
+process index_fasta {
+  tag "$fasta.baseName"
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_file
+
+  output:
+    file "*.index*" into index_files
+
+  script:
+"""
+hisat2-build ${fasta} ${fasta.baseName}.index
+"""
+}
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+params.index = "$baseDir/data/index/*.index*"
+
+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/", mode: 'copy'
+
+  input:
+  file reads from fastq_files
+  file index from index_files.toList()
+
+  output:
+  file "*" into count_files
+
+  script:
+"""
+hisat2 -x ${file(file(index[0]).baseName).baseName} -U ${reads} -S ${reads.baseName}.sam -p ${task.cpus}
+"""
+}
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$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: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$reads"
+  //tag "$index.baseName"
+  cpus 4
+  publishDir "results/mapping/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+  file index from index_files.toList()
+
+  output:
+  file "*" into counts_files
+
+  script:
+"""
+hisat2 -x ${file(file(index[0]).baseName).baseName} -1 ${reads[0]} -2 ${reads[1]} -S ${pair_id}.sam -p ${task.cpus}
+"""
+}
+
+/*
+* converting sam into bam
+*/
+
+/*                      sam to bam                                    */
+params.sam = "$baseDir/data/bam/*.sam"
+
+log.info "sam files : ${params.sam}"
+
+Channel
+  .fromPath( params.sam )
+  .ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
+  .set { sam_files }
+
+process bam_converter {
+  tag "$sam"
+  cpus 4
+  publishDir "results/mapping/bam/", mode: 'copy'
+
+  input:
+    file sam from sam_files
+
+  output:
+    file "*.bam" into bam_files
+
+  script:
+"""
+samtools view -@ ${task.cpus} -bS ${sam} > ${sam.baseName}.bam
+"""
+}