bedtools: add bam to fastq convertion

src/nf_modules/bedtools/main.nf

@@ -20,3 +20,43 @@ bedtools getfasta -name \
 -fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
 """
 }
+
+process bam_to_fastq_singleend {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bed.baseName}"
+  publishDir "results/fasta/", mode: 'copy'
+
+  input:
+  path fasta
+  path bed
+
+  output:
+  path "*_extracted.fasta", emit: fasta
+
+  script:
+"""
+bedtools bamtofastq
+-i ${bam} -fq ${bam.baseName}.fastq
+"""
+}
+
+process bam_to_fastq_paired_end {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bed.baseName}"
+  publishDir "results/fasta/", mode: 'copy'
+
+  input:
+  path fasta
+  path bed
+
+  output:
+  path "*_extracted.fasta", emit: fasta
+
+  script:
+"""
+bedtools bamtofastq
+-i ${bam} -fq ${bam.baseName}_R1.fastq -fq2 ${bam.baseName}_R2.fastq
+"""
+}