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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>
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: hisat2_align
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description: Align RNA-Seq reads to a reference with HISAT2
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keywords:
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- align
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- fasta
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- genome
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- reference
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tools:
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- hisat2:
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description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
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homepage: https://daehwankimlab.github.io/hisat2/
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documentation: https://daehwankimlab.github.io/hisat2/manual/
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doi: "10.1038/s41587-019-0201-4"
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: file
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description: HISAT2 genome index file
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pattern: "*.ht2"
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- splicesites:
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type: file
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description: Splices sites in gtf file
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pattern: "*.{txt}"
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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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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- summary:
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type: file
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description: Aligment log
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pattern: "*.log"
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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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- "@ntoda03"
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