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* 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 bamUtil trimBam * Update modules/bamutil/trimbam/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bamutil/trimbam/main.nf * Changes after code-review * YAML lint Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
51 lines
1.5 KiB
YAML
51 lines
1.5 KiB
YAML
name: bamutil_trimbam
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description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
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keywords:
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- bam
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- trim
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- clipping
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- bamUtil
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- trimBam
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tools:
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- bamutil:
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description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
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homepage: https://genome.sph.umich.edu/wiki/BamUtil
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documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
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tool_dev_url: https://github.com/statgen/bamUtil
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doi: "10.1101/gr.176552.114"
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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 file
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pattern: "*.bam"
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- trim_left:
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type: integer
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description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
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- trim_right:
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type: integer
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description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
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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: Trimmed but unsorted BAM file
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pattern: "*.bam"
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authors:
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- "@jfy133"
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