subworkflows/nfvalidation_plugin_utils

Sort SAM/BAM/CRAM file

sortbamsamcram

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

Description

Sort SAM/BAM/CRAM file

Input

Name (Type)

Description

Pattern

`ch_bam` (file)

The input channel containing the BAM/CRAM/SAM files
Structure: [ val(meta), path(bam) ]

*.{bam/cram/sam}

Output

Name (Type)

Description

Pattern

`bam` (file)

Channel containing BAM files
Structure: [ val(meta), path(bam) ]

*.bam

`bai` (file)

Channel containing indexed BAM (BAI) files
Structure: [ val(meta), path(bai) ]

*.bai

`csi` (file)

Channel containing CSI files
Structure: [ val(meta), path(csi) ]

*.csi

`versions` (file)

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml

subworkflows/nfvalidation_plugin_utils

Description

Input

`ch_bam` (file)

Output

`bam` (file)

`bai` (file)

`csi` (file)

`versions` (file)

included in

included modules and subworkflows

maintainer

get in touch

subworkflows/nfvalidation_plugin_utils

Description

Input

ch_bam (file)

Output

bam (file)

bai (file)

csi (file)

versions (file)

included in

included modules and subworkflows

maintainer

get in touch

`ch_bam` (file)

`bam` (file)

`bai` (file)

`csi` (file)

`versions` (file)