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fixed linting errors
This commit is contained in:
kevinmenden
parent
0eb20c14bf
commit
07f0a2476a
4 changed files with 36 additions and 36 deletions
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@ -1,3 +1,4 @@
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/*
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/*
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* -----------------------------------------------------
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* -----------------------------------------------------
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* Utility functions used in nf-core DSL2 module files
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* Utility functions used in nf-core DSL2 module files
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@ -1,3 +1,4 @@
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/*
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/*
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* -----------------------------------------------------
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* -----------------------------------------------------
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* Utility functions used in nf-core DSL2 module files
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* Utility functions used in nf-core DSL2 module files
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@ -7,45 +7,45 @@ keywords:
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- reference
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- reference
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tools:
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tools:
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- bowtie:
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- bowtie:
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description: |
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description: |
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bowtie is a software package for mapping DNA sequences against
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bowtie is a software package for mapping DNA sequences against
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a large reference genome, such as the human genome.
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a large reference genome, such as the human genome.
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homepage: http://bowtie-bio.sourceforge.net/index.shtml
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homepage: http://bowtie-bio.sourceforge.net/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/manual.shtml
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documentation: http://bowtie-bio.sourceforge.net/manual.shtml
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arxiv: arXiv:1303.3997
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arxiv: arXiv:1303.3997
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params:
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params:
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- outdir:
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- outdir:
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type: string
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type: string
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description: |
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description: |
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The pipeline's output directory. By default, the module will
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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- publish_dir_mode:
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type: string
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type: string
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description: |
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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- enable_conda:
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type: boolean
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type: boolean
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description: |
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description: |
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Run the module with Conda using the software specified
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Run the module with Conda using the software specified
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via the `conda` directive
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via the `conda` directive
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- singularity_pull_docker_container:
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- singularity_pull_docker_container:
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type: boolean
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type: boolean
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description: |
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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force the workflow to pull and convert Docker containers instead.
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input:
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input:
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- fasta:
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- fasta:
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type: file
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type: file
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description: Input genome fasta file
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description: Input genome fasta file
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output:
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output:
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- index:
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- index:
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type: file
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type: file
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description: Bowtie genome index files
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description: Bowtie genome index files
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pattern: "*.ebwt"
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pattern: "*.ebwt"
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- version:
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- version:
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type: file
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type: file
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description: File containing software version
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description: File containing software version
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pattern: "*.{version.txt}"
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pattern: "*.{version.txt}"
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authors:
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authors:
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- "@kevinmenden"
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- "@kevinmenden"
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@ -17,7 +17,7 @@
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- path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
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- path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
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md5sum: f3c398bba5158f4039334a932d79c051
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md5sum: f3c398bba5158f4039334a932d79c051
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- name: Run bowtie index and align signle-end
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- name: Run bowtie index and align single-end
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
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tags:
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tags:
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- bowtie
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- bowtie
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@ -40,8 +40,7 @@
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- path: output/bowtie/test.bam
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- path: output/bowtie/test.bam
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md5sum: 8179c68a819accbc9137dc881736106f
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md5sum: 8179c68a819accbc9137dc881736106f
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- name: Run bowtie index and align paired-end
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- name: Run bowtie index and align paired_end
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
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tags:
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tags:
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- bowtie
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- bowtie
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@ -63,4 +62,3 @@
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md5sum: a23e9a2a76e949aeb3693bcfae41a615
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md5sum: a23e9a2a76e949aeb3693bcfae41a615
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- path: output/bowtie/test.bam
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- path: output/bowtie/test.bam
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md5sum: 9ce5aebf37128f4bb1d24e9548e22009
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md5sum: 9ce5aebf37128f4bb1d24e9548e22009
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