nf-core_modules/modules/leehom/meta.yml

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Add `leehom` module (#1052) * 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>
2021-11-15 14:26:06 +00:00
name: leehom
description: Bayesian reconstruction of ancient DNA fragments
keywords:
- ancient DNA
- adapter removal
- clipping
- trimming
- merging
- collapsing
- preprocessing
- bayesian
tools:
- leehom:
description: Bayesian reconstruction of ancient DNA fragments
homepage: "https://grenaud.github.io/leeHom/"
documentation: "https://github.com/grenaud/leeHom"
tool_dev_url: "https://github.com/grenaud/leeHom"
doi: "10.1093/nar/gku699"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: Unaligned BAM or one or two gzipped FASTQ file(s)
pattern: "*.{bam,fq.gz,fastq.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: BAM file
pattern: "*.bam"
- fq_pass:
type: file
description: Trimmed and merged FASTQ
pattern: "*.fq.gz"
- fq_fail:
type: file
description: Failed trimmed and merged FASTQs
pattern: "*.fail.fq.gz"
- unmerged_r1_fq_pass:
type: file
description: Passed unmerged R1 FASTQs
pattern: "*.r1.fq.gz"
- unmerged_r1_fq_fail:
type: file
description: Failed unmerged R1 FASTQs
pattern: "*.r1.fail.fq.gz"
- unmerged_r2_fq_pass:
type: file
description: Passed unmerged R1 FASTQs
pattern: "*.r2.fq.gz"
- unmerged_r2_fq_pass:
type: file
description: Failed unmerged R1 FASTQs
pattern: "*.r2.fail.fq.gz"
- log:
type: file
description: Log file of command
pattern: "*.log"
authors:
- "@jfy133"