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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>
54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
name: arriba
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description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
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keywords:
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- fusion
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- arriba
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tools:
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- arriba:
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description: Fast and accurate gene fusion detection from RNA-Seq data
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homepage: https://github.com/suhrig/arriba
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documentation: https://arriba.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/suhrig/arriba
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doi: "10.1101/gr.257246.119"
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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: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- fasta:
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type: file
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description: Assembly FASTA file
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pattern: "*.{fasta}"
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- gtf:
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type: file
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description: Annotation GTF file
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pattern: "*.{gtf}"
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output:
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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', 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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- fusions:
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type: file
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description: File contains fusions which pass all of Arriba's filters.
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pattern: "*.{fusions.tsv}"
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- fusions_fail:
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type: file
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description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.
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pattern: "*.{fusions.discarded.tsv}"
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authors:
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- "@praveenraj2018"
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