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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>
105 lines
3.4 KiB
YAML
105 lines
3.4 KiB
YAML
name: gatk4_mutect2
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description: Call somatic SNVs and indels via local assembly of haplotypes.
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keywords:
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- gatk4
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- mutect2
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- haplotype
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- somatic
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ["Apache-2.0"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test']
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- input:
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type: list
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description: list of BAM files, also able to take CRAM as an input
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pattern: "*.{bam/cram}"
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- input_index:
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type: list
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description: list of BAM file indexes, also able to take CRAM indexes as an input
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pattern: "*.{bam.bai/cram.crai}"
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- intervals:
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type: File/string
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description: Specify region the tools is run on.
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pattern: ".{bed,interval_list}/chrM"
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- which_norm:
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type: list
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description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode)
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pattern: "testN"
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- run_single:
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type: boolean
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description: Specify whether or not to run in tumor_single mode instead of tumor_normal_pair mode (will be ignored if run_pon is also true)
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pattern: "true/false"
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- run_pon:
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type: boolean
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description: Specify whether or not to run in panel_of_normal mode instead of tumor_normal_pair mode
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pattern: "true/false"
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- run_mito:
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type: boolean
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description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode
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pattern: "true/false"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- germline_resource:
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type: file
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description: Population vcf of germline sequencing, containing allele fractions.
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pattern: "*.vcf.gz"
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- germline_resource_tbi:
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type: file
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description: Index file for the germline resource.
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pattern: "*.vcf.gz.tbi"
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- panel_of_normals:
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type: file
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description: vcf file to be used as a panel of normals.
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pattern: "*.vcf.gz"
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- panel_of_normals_tbi:
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type: file
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description: Index for the panel of normals.
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pattern: "*.vcf.gz.tbi"
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output:
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- vcf:
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type: file
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description: compressed vcf file
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: Index of vcf file
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pattern: "*vcf.gz.tbi"
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- stats:
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type: file
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description: Stats file that pairs with output vcf file
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pattern: "*vcf.gz.stats"
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- f1r2:
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type: file
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description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)
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pattern: "*.f1r2.tar.gz"
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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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authors:
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- "@GCJMackenzie"
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