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fixed linting errors

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kevinmenden 2020-12-18 09:50:05 +01:00
parent 0eb20c14bf
commit 07f0a2476a
4 changed files with 36 additions and 36 deletions
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1
software/bowtie/align/functions.nf
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@ -1,3 +1,4 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files

1
software/bowtie/index/functions.nf
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@ -1,3 +1,4 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files

60
software/bowtie/index/meta.yml
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@ -7,45 +7,45 @@ keywords:
- reference
tools:
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- fasta:
type: file
description: Input genome fasta file
type: file
description: Input genome fasta file
output:
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"

6
tests/software/bowtie/test.yml
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@ -17,7 +17,7 @@
- path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- name: Run bowtie index and align signle-end
- name: Run bowtie index and align single-end
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags:
- bowtie
@ -40,8 +40,7 @@
- path: output/bowtie/test.bam
md5sum: 8179c68a819accbc9137dc881736106f
- name: Run bowtie index and align paired_end
- name: Run bowtie index and align paired-end
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
tags:
- bowtie
@ -63,4 +62,3 @@
md5sum: a23e9a2a76e949aeb3693bcfae41a615
- path: output/bowtie/test.bam
md5sum: 9ce5aebf37128f4bb1d24e9548e22009