bam_qc_picard

Produces comprehensive statistics from BAM file

statisticscountshs_metricswgs_metricsbamsamcram

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

Description

Produces comprehensive statistics from BAM file

Input

name

description

pattern

`meta`

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

`bam`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bai`

BAM/CRAM/SAM file index

*.{bai,crai,sai}

`bait_intervals`

An interval list or bed file that contains the locations of the baits used.

baits.{interval_list,bed,bed.gz}

`target_intervals`

An interval list or bed file that contains the locations of the targets.

targets.{interval_list,bed,bed.gz}

`meta2`

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

`fasta`

Reference fasta file

*.{fasta,fa,fna}

`meta2`

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

`fasta_fai`

Reference fasta file index

*.{fasta,fa,fna}.fai

`meta2`

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

`fasta_dict`

Reference fasta sequence dictionary

*.{dict}

Output

name

description

pattern

`meta`

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

`coverage_metrics`

Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics

*_metrics.txt

`multiple_metrics`

Alignment metrics files generated by picard CollectMultipleMetrics

*_{metrics}

`versions`

File containing software versions

versions.yml