Align reads to a reference genome using bwa then sort with samtools
ch_reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. Structure: [ val(meta), [ path(reads) ] ]
ch_index
BWA genome index files Structure: [ val(meta), path(index) ]
val_sort_bam
If true bwa modules sort resulting bam files
true|false
ch_fasta
Optional reference fasta file. This only needs to be given if val_sort_bam = true. Structure: [ val(meta), path(fasta) ]
bam_orig
BAM file produced by bwa Structure: [ val(meta), path(bam) ]
bam
BAM file ordered by samtools Structure: [ val(meta), path(bam) ]
bai
BAI index of the ordered BAM file Structure: [ val(meta), path(bai) ]
csi
CSI index of the ordered BAM file Structure: [ val(meta), path(csi) ]
stats
File containing samtools stats output Structure: [ val(meta), path(stats) ]
flagstat
File containing samtools flagstat output Structure: [ val(meta), path(flagstat) ]
idxstats
File containing samtools idxstats output Structure: [ val(meta), path(idxstats) ]
versions
Files containing software versions Structure: [ path(versions.yml) ]
