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2c3c87a10f
* 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 leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
77 lines
1.9 KiB
YAML
77 lines
1.9 KiB
YAML
name: leehom
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description: Bayesian reconstruction of ancient DNA fragments
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keywords:
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- ancient DNA
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- adapter removal
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- clipping
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- trimming
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- merging
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- collapsing
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- preprocessing
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- bayesian
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tools:
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- leehom:
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description: Bayesian reconstruction of ancient DNA fragments
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homepage: "https://grenaud.github.io/leeHom/"
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documentation: "https://github.com/grenaud/leeHom"
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tool_dev_url: "https://github.com/grenaud/leeHom"
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doi: "10.1093/nar/gku699"
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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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- reads:
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type: file
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description: Unaligned BAM or one or two gzipped FASTQ file(s)
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pattern: "*.{bam,fq.gz,fastq.gz}"
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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: BAM file
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pattern: "*.bam"
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- fq_pass:
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type: file
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description: Trimmed and merged FASTQ
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pattern: "*.fq.gz"
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- fq_fail:
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type: file
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description: Failed trimmed and merged FASTQs
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pattern: "*.fail.fq.gz"
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- unmerged_r1_fq_pass:
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type: file
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description: Passed unmerged R1 FASTQs
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pattern: "*.r1.fq.gz"
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- unmerged_r1_fq_fail:
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type: file
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description: Failed unmerged R1 FASTQs
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pattern: "*.r1.fail.fq.gz"
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- unmerged_r2_fq_pass:
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type: file
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description: Passed unmerged R1 FASTQs
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pattern: "*.r2.fq.gz"
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- unmerged_r2_fq_pass:
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type: file
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description: Failed unmerged R1 FASTQs
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pattern: "*.r2.fail.fq.gz"
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- log:
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type: file
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description: Log file of command
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pattern: "*.log"
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authors:
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- "@jfy133"
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