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yevis-metadata_gatk-workflows_mitochondria-pipeline.yml
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yevis-metadata_gatk-workflows_mitochondria-pipeline.yml
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---
id: 68c32f9c-bdaa-420c-879c-90b40d8bc4d5
version: 1.0.0
license: CC0-1.0
authors:
- github_account: suecharo
name: Hirotaka Suetake
affiliation: "The University of Tokyo"
orcid: 0000-0003-2765-0049
workflow:
name: GATK workflows - Mitochondria Pipeline
readme: "https://raw.githubusercontent.com/broadinstitute/gatk/bd640eaf935c56155c4caa23922a96cfd5f14b6e/README.md"
language:
type: WDL
version: "1.0"
files:
- url: "https://raw.githubusercontent.com/broadinstitute/gatk/bd640eaf935c56155c4caa23922a96cfd5f14b6e/scripts/mitochondria_m2_wdl/AlignAndCall.wdl"
target: AlignAndCall.wdl
type: secondary
- url: "https://raw.githubusercontent.com/broadinstitute/gatk/bd640eaf935c56155c4caa23922a96cfd5f14b6e/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl"
target: AlignmentPipeline.wdl
type: secondary
- url: "https://raw.githubusercontent.com/broadinstitute/gatk/bd640eaf935c56155c4caa23922a96cfd5f14b6e/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl"
target: MitochondriaPipeline.wdl
type: primary
testing:
- id: example_test
files:
- url: "https://gist.github.com/69b0086317263b7160bb492914f4a07d"
target: wf_params.json
type: wf_params
- url: "https://storage.googleapis.com/gatk-best-practices/mitochondria-pipeline/G97753.NA12878.bam"
type: other
- url: "https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/assets/G97753.NA12878.bai"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.dict"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.fai"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.amb"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.ann"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.bwt"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.pac"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.sa"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/blacklist_sites.hg38.chrM.bed"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/blacklist_sites.hg38.chrM.bed.idx"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/ShiftBack.chain"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/control_region_shifted.chrM.interval_list"
type: other
- url: "https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/chrM/non_control_region.chrM.interval_list"
type: other