modules/picard_cleansam

Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads

cleanbampicardsamclipping

https://github.com/nf-core/modules/[...]/modules/nf-core/picard/cleansam

Description

Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads

Input

name:type

description

pattern

`meta:map`

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

`bam:file`

BAM file

*.{bam}

Output

name:type

description

pattern

`bam`

`meta:map`

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

`*.bam:file`

Cleaned BAM file

*.{bam}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- https://github.com/broadinstitute/picard

modules/picard_cleansam

Description

Input

meta:map

bam:file

Output

bam

meta:map

*.bam:file

versions

versions.yml:file

Tools

picard MIT

`meta:map`

`bam:file`

`bam`

`meta:map`

`*.bam:file`

`versions`

`versions.yml:file`

picard
MIT