bam_sort_stats_samtools

Sort SAM/BAM/CRAM file

sortbamsamcram

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_sort_stats_samtools

Description

Sort SAM/BAM/CRAM file

Input

name

description

pattern

`ch_bam`

BAM/CRAM/SAM file.

Structure: [ val(meta), path(bam) ]

*.{bam,cram,sam}

`ch_fasta_fai`

Reference genome fasta file and its index.

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

*.{fasta,fa}

Output

name

description

pattern

`bam`

Sorted BAM/CRAM/SAM file.

Structure: [ val(meta), path(bam) ]

*.{bam,cram,sam}

`index`

BAM/CRAM/SAM index file.

Structure: [ val(meta), path(index) ]

*.{bai,crai,csi}

`stats`

File containing samtools stats output.

Structure: [ val(meta), path(stats) ]

*.stats

`flagstat`

File containing samtools flagstat output.

Structure: [ val(meta), path(flagstat) ]

*.flagstat

`idxstats`

File containing samtools idxstats output.

Structure: [ val(meta), path(idxstats) ]

*.idxstats