bam_sort_stats_samtools

Sort SAM/BAM/CRAM file

sortbamsamcram

Description

Sort SAM/BAM/CRAM file

name

description

pattern

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

BAM/CRAM/SAM file

*.{bam,cram,sam}

Reference genome fasta file

*.{fasta,fa}

name

description

pattern

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

BAM/CRAM/SAM index file

*.{bai,crai,sai}

BAM/CRAM/SAM index file

*.{bai,crai,sai}

File containing samtools stats output

*.{stats}

File containing samtools flagstat output

*.{flagstat}

File containing samtools idxstats output

*.{idxstats}

File containing software versions

versions.yml