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801240a971
* create files with nf-core command * update meta.yml files * starting to work on index main.nf * prelim test for index * index test working; not finding all output files * index passing tests * index and align passing tests * prototyping biscuitblaster and pileup * update containers * updates to pileup * pileup passing tests * template creation for more biscuit tools * tests passing on blaster,bsconv,pupsom * epiread passing tests, but need to update SNP bed file path * vcf2bed working; change test file * all biscuit commands passing tests * biscuitblaster rename * try to fix permissions * more permission fixes * trying a couple more permission changes * hopefully last permission fixes * really last permission changes * few more permissions * add when blocks * Remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * changes for first round of review * update meta.yml with more specific links * Update modules/biscuit/biscuitblaster/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Apply new version reporting Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/pileup/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf * Update modules/biscuit/pileupsomatic/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * update test file path * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * tests passing again * Update modules/biscuit/align/main.nf * Update modules/biscuit/bsconv/main.nf * Update modules/biscuit/epiread/main.nf * Update modules/biscuit/index/main.nf * Update test.yml * Update modules/biscuit/pileupsomatic/main.nf * remove module-specific extension/prefix * remove module-specific extension/prefix * add missing args * switch pileup strategy * update test.yml * remove debug * whitespace cleanup * add in newline escapes * requested changes * Update modules/biscuit/pileup/meta.yml Co-authored-by: Spix <nathan.spix@submit.cm.cluster> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Spix <nathan.spix@node107.cm.cluster> Co-authored-by: njspix <nathan.spix@vai.org>
70 lines
2.4 KiB
YAML
70 lines
2.4 KiB
YAML
name: biscuit_pileup
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description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
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keywords:
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- bisulfite
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- DNA methylation
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- pileup
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- variant calling
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- WGBS
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- scWGBS
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- bam
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- vcf
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tools:
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- biscuit:
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description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
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homepage: https://huishenlab.github.io/biscuit/
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documentation: https://huishenlab.github.io/biscuit/docs/pileup.html
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tool_dev_url: https://github.com/huishenlab/biscuit
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doi: ""
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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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- normal_bams:
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type: file(s)
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description: |
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BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
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("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
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tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
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pattern: "*.{bam}"
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- normal_bais:
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type: file(s)
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description: BAM index file or files corresponding to the provided normal_bams
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pattern: "*.{bai}"
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- tumor_bam:
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type: file(s)
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description: |
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Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
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their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
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tumor BAM file is provided, exactly one normal BAM must be provided.
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pattern: "*.{bam}"
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- tumor_bai:
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type: file(s)
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description: Optional. BAM index file corresponding to provided tumor_bam
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pattern: "*.{bai}"
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- index:
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type: dir
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description: Biscuit genome index directory (generated with 'biscuit index')
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pattern: "BiscuitIndex"
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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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- vcf:
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type: file
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description: vcf file with methylation information
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pattern: "*.{vcf.gz}"
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authors:
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- "@njspix"
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