nf-core_modules/modules/samtools/merge/meta.yml
FriederikeHanssen ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +02:00

54 lines
1.5 KiB
YAML

name: samtools_merge
description: Merge BAM or CRAM file
keywords:
- merge
- bam
- sam
- cram
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_files:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.{bam}"
- cram:
type: file
description: CRAM file
pattern: "*.{cram}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@yuukiiwa "
- "@maxulysse"
- "@FriederikeHanssen"