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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>
58 lines
1.5 KiB
YAML
58 lines
1.5 KiB
YAML
name: biscuit_epiread
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description: |
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Summarizes read-level methylation (and optionally SNV) information from a
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Biscuit BAM file in a standard-compliant BED format.
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keywords:
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- biscuit
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- DNA methylation
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- WGBS
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- scWGBS
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- bisulfite sequencing
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- aligner
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- bam
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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/epiread_format/
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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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- bam:
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type: file
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description: Biscuit BAM file
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- bai:
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type: file
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description: BAM index
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- snp_bed:
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type: file
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description: BED file containing SNP information (optional)
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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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- epiread_bed:
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type: file
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description: Gzipped BED file with methylation (and optionally SNV) information
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pattern: "*.{epiread.bed.gz}"
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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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authors:
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- "@njspix"
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