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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>
50 lines
1.3 KiB
YAML
50 lines
1.3 KiB
YAML
name: metabat2_jgisummarizebamcontigdepths
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description: Depth computation per contig step of metabat2
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keywords:
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- sort
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- binning
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- depth
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- bam
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- coverage
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- de novo assembly
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tools:
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- metabat2:
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description: Metagenome binning
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homepage: https://bitbucket.org/berkeleylab/metabat/src/master/
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documentation: https://bitbucket.org/berkeleylab/metabat/src/master/
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tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/
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doi: "10.7717/peerj.7359"
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licence: ["BSD-3-clause-LBNL"]
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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: Sorted BAM file of reads aligned on the assembled contigs
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pattern: "*.bam"
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- bai:
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type: file
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description: BAM index file
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pattern: "*.bam.bai"
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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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- depth:
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type: file
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description: Text file listing the coverage per contig
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pattern: ".txt.gz"
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authors:
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- "@maxibor"
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