nf-core_modules/modules/bismark/genomepreparation/meta.yml

name: bismark_genomepreparation
description: |
  Converts a specified reference genome into two different bisulfite
  converted versions and indexes them for alignments.
keywords:
  - bismark
  - 3-letter genome
  - index
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - fasta
tools:
  - bismark:
      description: |
        Bismark is a tool to map bisulfite treated sequencing reads
        and perform methylation calling in a quick and easy-to-use fashion.
      homepage: https://github.com/FelixKrueger/Bismark
      documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
      doi: 10.1093/bioinformatics/btr167
      licence: ["GPL-3.0-or-later"]
input:
  - fasta:
      type: file
      description: Input genome fasta file
output:
  - index:
      type: dir
      description: Bismark genome index directory
      pattern: "BismarkIndex"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names 2021-03-22 16:46:11 +00:00			`name: bismark_genomepreparation`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`description: \|`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`Converts a specified reference genome into two different bisulfite`
			`converted versions and indexes them for alignments.`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`keywords:`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`- bismark`
			`- 3-letter genome`
			`- index`
			`- methylation`
			`- 5mC`
			`- methylseq`
			`- bisulphite`
			`- fasta`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`tools:`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`- bismark:`
			`description: \|`
			`Bismark is a tool to map bisulfite treated sequencing reads`
			`and perform methylation calling in a quick and easy-to-use fashion.`
			`homepage: https://github.com/FelixKrueger/Bismark`
			`documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs`
			`doi: 10.1093/bioinformatics/btr167`
			`licence: ["GPL-3.0-or-later"]`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`input:`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`- fasta:`
			`type: file`
			`description: Input genome fasta file`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`output:`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`- index:`
			`type: dir`
			`description: Bismark genome index directory`
			`pattern: "BismarkIndex"`
			`- versions:`
			`type: file`
			`description: File containing software versions`
			`pattern: "versions.yml"`
add bismark/genome_preparation + tests 2021-02-18 09:56:36 +00:00			`authors:`
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2022-02-15 11:15:27 +00:00			`- "@phue"`