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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
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description: convert between genome builds
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keywords:
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- liftOver
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- picard
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tools:
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- picard:
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description: Move annotations from one assembly to another
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homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
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documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
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tool_dev_url: https://github.com/broadinstitute/picard
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doi: ""
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input_vcf:
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type: file
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description: VCF file
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pattern: "*.{vcf,vcf.gz}"
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- chain:
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type: file
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description: The liftover chain file
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- fasta:
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type: file
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description: fasta file
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pattern: "*.fasta"
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- dict:
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type: file
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description: dictionary for fasta file
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pattern: "*.{dict}"
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output:
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- meta:
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type: map
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description: Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- vcf_lifted:
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type: file
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description: VCF file containing successfully lifted variants
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pattern: "*.{lifted.vcf.gz}"
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- vcf_unlifted:
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type: file
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description: VCF file containing unsuccessfully lifted variants
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pattern: "*.{unlifted.vcf.gz}"
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authors:
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- "@lucpen"
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