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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>
67 lines
1.7 KiB
YAML
67 lines
1.7 KiB
YAML
name: pbccs
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description: Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads
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keywords:
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- ccs
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tools:
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- pbccs:
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description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
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homepage: https://github.com/PacificBiosciences/pbbioconda
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documentation: https://ccs.how/
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tool_dev_url: https://github.com/PacificBiosciences/ccs
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doi: ""
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licence: ["BSD-3-Clause-Clear"]
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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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id: id of the split file
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- bam:
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type: file
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description: Raw subreads bam
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pattern: "*.subreads.bam"
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- pbi:
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type: file
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description: Pacbio BAM Index
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pattern: "*.pbi"
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- chunk_num:
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-type: integer
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-description: BAM part to process
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- chunk_on:
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-type: integer
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-description: Total number of bam parts to process
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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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- bam:
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type: file
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description: CCS sequences in bam format
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pattern: "*.bam"
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- pbi:
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type: file
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description: PacBio Index of CCS sequences
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pattern: "*.pbi"
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- report_txt:
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type: file
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description: Summary of CCS in txt format
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pattern: ".txt"
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- report_json:
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type: file
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description: Summary of CCS in txt json
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pattern: ".json"
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- metrics:
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type: file
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description: Metrics about zmws
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pattern: "*.json.gz"
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authors:
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- "@sguizard"
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