BWA_MEM module

params.options

• publish_dir, publish directory, default 'bwa/mem'
• publish_mode, publish mode, default 'copy'
• publish_enabled, publish enabled, defaults false
• args, arguments for bwa mem command, default "-M"
• samtools_args, arguments for samtools view command, default "-h -F 0x0100 -O BAM"
• suffix, suffix for output file name, default ""

labels

• process_high

input

• tuple val(meta), path(reads)
• tuple path(index), path(fasta)

output

• tuple val(meta), path("*.bam"), emit: bam
• path "bwa.version.txt", emit: version