mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
53 lines
1.7 KiB
YAML
53 lines
1.7 KiB
YAML
name: samblaster
|
|
description: |
|
|
This module combines samtools and samblaster in order to use
|
|
samblaster capability to filter or tag SAM files, with the advantage
|
|
of maintaining both input and output in BAM format.
|
|
Samblaster input must contain a sequence header: for this reason it has been piped
|
|
with the "samtools view -h" command.
|
|
Additional desired arguments for samtools can be passed using:
|
|
options.args2 for the input bam file
|
|
options.args3 for the output bam file
|
|
keywords:
|
|
- sort
|
|
tools:
|
|
- samblaster:
|
|
description: |
|
|
samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.
|
|
It can also optionally output discordant read pairs and/or split read mappings to separate SAM files,
|
|
and/or unmapped/clipped reads to a separate FASTQ file.
|
|
By default, samblaster reads SAM input from stdin and writes SAM to stdout.
|
|
homepage: None
|
|
documentation: https://github.com/GregoryFaust/samblaster
|
|
tool_dev_url: https://github.com/GregoryFaust/samblaster
|
|
doi: "10.1093/bioinformatics/btu314"
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM file
|
|
pattern: "*.bam"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: Tagged or filtered BAM file
|
|
pattern: "*.bam"
|
|
|
|
authors:
|
|
- "@lescai"
|