The pipeline converts unmapped BAMs downloaded from the European Genome-Phenome Archive. It takes files from ../data/bam/*.bam and converts them into fastq files, runs FastQC and produces a MultiQC report in ../data/fastq.
This follows the samtools fastq man page by first sorting by name (-n), then piping to samtools fastq. If the reads are paired, forward and reverse reads are emitted to *_R1.fastq.gz and *_R2.fastq.gz respectively. Read names are appended with /1 and /2 (-N). Singletons (unmatched reads) are discarded. When reads are single-ended, they are emitted to *_R0.fastq.gz.
samtools sort -@ ${task.cpus} -n ${bam} | samtools fastq -1 ${name}_R1.fastq.gz -2 ${name}_R2.fastq.gz -0 ${name}_R0.fastq.gz -s /dev/null -N -F 0x900 -To run the pipeline, make sure nextflow and singularity are available in the $PATH, then:
nextflow run drejom/bam2fastq-nfThe input locations can be changed at runtime by setting --bams to a quoted, globbed, relative or absolute path (eg --bams 'downloads/*.bam'); similarly the location of the output can be set with the --output parameter.