mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
f079367416
* Building Picard liftovervcf module * Building Picard liftovervcf module_test * Building Picard liftovervcf pytest * Module for picard liftover vcf created * Fixed files after linting test * Fixed trailing whitespace * Checked files with prettier * further formatting with prettier * Fixed test.yml * Fixed input variable names * Changed contain test.liftef.vcf * Changed contain in test.yml test.liftef.vcf * Run prittier * Going back to previous version of test.yml * downgrading picard to 2.26.10 from 2.26.11 * Update modules/picard/liftovervcf/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Print available memory Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Output from .vcf to .vcf.gz * Added spaces to align emit * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Removing md5sum test Co-authored-by: jemten <jemten@users.noreply.github.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: picard_liftovervcf
|
|
description: convert between genome builds
|
|
keywords:
|
|
- liftOver
|
|
- picard
|
|
tools:
|
|
- picard:
|
|
description: Move annotations from one assembly to another
|
|
homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
|
|
tool_dev_url: https://github.com/broadinstitute/picard
|
|
doi: ""
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- input_vcf:
|
|
type: file
|
|
description: VCF file
|
|
pattern: "*.{vcf,vcf.gz}"
|
|
- chain:
|
|
type: file
|
|
description: The liftover chain file
|
|
- fasta:
|
|
type: file
|
|
description: fasta file
|
|
pattern: "*.fasta"
|
|
- dict:
|
|
type: file
|
|
description: dictionary for fasta file
|
|
pattern: "*.{dict}"
|
|
|
|
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"
|
|
- vcf_lifted:
|
|
type: file
|
|
description: VCF file containing successfully lifted variants
|
|
pattern: "*.{lifted.vcf.gz}"
|
|
- vcf_unlifted:
|
|
type: file
|
|
description: VCF file containing unsuccessfully lifted variants
|
|
pattern: "*.{unlifted.vcf.gz}"
|
|
|
|
authors:
|
|
- "@lucpen"
|