Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats
ch_reads
Sequence reads in BAM/CRAM/SAM format Structure: [ val(meta), path(reads) ]
ch_fasta
Reference genome fasta file required for CRAM input Structure: [ path(fasta) ]
Index of the reference genome fasta file Structure: [ path(fai) ]
bam
processed BAM/SAM file Structure: [ val(meta), path(bam) ]
bai
BAM/SAM samtools index Structure: [ val(meta), path(bai) ]
cram
processed CRAM file Structure: [ val(meta), path(cram) ]
crai
CRAM samtools index Structure: [ val(meta), path(crai) ]
csi
CSI samtools index 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) ]
