nf-core_modules/modules/hmmcopy/generatemap/meta.yml

name: hmmcopy_generatemap
description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
keywords:
  - hmmcopy
  - mapcounter
  - mappability
tools:
  - hmmcopy:
      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
      homepage: https://github.com/shahcompbio/hmmcopy_utils
      documentation: https://github.com/shahcompbio/hmmcopy_utils
      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
      doi: ""
      licence: ["GPL v3"]

input:
  - fasta:
      type: file
      description: Input genome fasta file

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bigwig:
      type: file
      description: bigwig file containing the mappability of the genome
      pattern: "*.{map.bw}"

authors:
  - "@sppearce"
New subtool: hmmcopy/generatemap (#1168) * Initial structure * Working with local singularity image * Working generateMap.pl script * Remote not working bioconda * Working generateMap with biocontainer * Lint changes * Updated hmmcopy container version to be consistent * Fix failing test * Remove path to perl * No hardpath to script * Update main.nf Moved version outside of process, add support for zipped fasta file * Revert to not allowing gzip via pipe, as perl script can't cope Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> 2021-12-15 15:57:42 +00:00			`name: hmmcopy_generatemap`
			`description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.`
			`keywords:`
			`- hmmcopy`
			`- mapcounter`
			`- mappability`
			`tools:`
			`- hmmcopy:`
			`description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy`
			`homepage: https://github.com/shahcompbio/hmmcopy_utils`
			`documentation: https://github.com/shahcompbio/hmmcopy_utils`
			`tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils`
			`doi: ""`
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			`licence: ["GPL v3"]`
New subtool: hmmcopy/generatemap (#1168) * Initial structure * Working with local singularity image * Working generateMap.pl script * Remote not working bioconda * Working generateMap with biocontainer * Lint changes * Updated hmmcopy container version to be consistent * Fix failing test * Remove path to perl * No hardpath to script * Update main.nf Moved version outside of process, add support for zipped fasta file * Revert to not allowing gzip via pipe, as perl script can't cope Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> 2021-12-15 15:57:42 +00:00
			`input:`
			`- fasta:`
			`type: file`
			`description: Input genome fasta file`

			`output:`
			`- versions:`
			`type: file`
			`description: File containing software versions`
			`pattern: "versions.yml"`
			`- bigwig:`
			`type: file`
			`description: bigwig file containing the mappability of the genome`
			`pattern: "*.{map.bw}"`

			`authors:`
			`- "@sppearce"`