src/nf_modules/Hisat2/test/bam_converter.nf : converting sam to bam

src/nf_modules/Hisat2/test/bam_converter.nf

+/*
+* SAMtools :
+* Imputs : sam files
+* Output : bam files
+*/
+
+/*                      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
+"""
+}