bam_variant_calling_sort_freebayes_bcftools

Alignments to call variants from, where input1 is a BAM/CRAM/SAM file with its
index index1, input2 is an optional second BAM/CRAM/SAM file with its index
index2 used to run variant calling with a pair (normal vs tumour), and bed is
an optional BED file limiting the analysis to the targets listed in it.

Structure: [ val(meta), path(input1), path(index1), path(input2), path(index2), path(bed) ]

Reference fasta file and its index.

Structure: [ val(meta2), path(fasta), path(fai) ]

Optional - Limit analysis to samples listed (one per line) in the file.

Structure: [ val(meta3), path(samples) ]

Optional - Each line of the file should list a sample and a population which it is part of.

Structure: [ val(meta4), path(populations) ]

Optional - A copy number map BED file, which has either a sample-level ploidy:
sample_name copy_number
or a region-specific format:
seq_name start end sample_name copy_number

Structure: [ val(meta5), path(cnv) ]