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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>
52 lines
1.3 KiB
YAML
52 lines
1.3 KiB
YAML
name: ultra_pipeline
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description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection
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keywords:
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- uLTRA
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- minimap2
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tools:
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- ultra:
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description: Splice aligner of long transcriptomic reads to genome.
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homepage: https://github.com/ksahlin/uLTRA
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documentation: https://github.com/ksahlin/uLTRA
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tool_dev_url: https://github.com/ksahlin/uLTRA
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doi: "10.1093/bioinformatics/btab540"
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licence: ["GNU GPLV3"]
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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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- reads:
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type: file
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description: A fasta or fastq file of reads to align
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pattern: "*.{fasta,fastq}"
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- genome:
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type: file
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description: fasta file of reference genome
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pattern: "*.fasta"
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- gtf:
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type: file
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description: A annotation of use the genome
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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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- sam:
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type: file
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description: The aligned reads in sam format
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pattern: "*.sam"
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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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- "@sguizard"
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- "@lassefolkersen"
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- "@ksahlin"
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