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e27553b989
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add dedup (tests and version not working) * Fix dedup and tests Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
60 lines
1.5 KiB
YAML
60 lines
1.5 KiB
YAML
name: dedup
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description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
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keywords:
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- dedup
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- deduplication
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- pcr duplicates
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- ancient DNA
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- paired-end
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- bam
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tools:
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- dedup:
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description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
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homepage: https://github.com/apeltzer/DeDup
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documentation: https://dedup.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/apeltzer/DeDup
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doi: "10.1186/s13059-016-0918-z"
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licence: ['GPL v3']
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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/SAM file
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pattern: "*.{bam,sam}"
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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: Deduplicated BAM file
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pattern: "*_rmdup.bam"
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- json:
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type: file
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description: JSON file for MultiQC
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pattern: "*.json"
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- hist:
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type: file
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description: Histogram data of amount of deduplication
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pattern: "*.hist"
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- log:
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type: file
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description: Dedup log information
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pattern: "*log"
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authors:
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- "@jfy133"
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