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Update indents and syntax
This commit is contained in:
drpatelh
parent
29f1585068
commit
736a0aa43c
8 changed files with 317 additions and 314 deletions
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@ -1,52 +1,52 @@
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name: bwa_index
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description: Create BWA index for reference genome
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keywords:
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- index
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- fasta
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- genome
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- index
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- fasta
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- genome
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- reference
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tools:
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- bwa:
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description: |
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BWA 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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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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- bwa:
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description: |
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BWA 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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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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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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- conda:
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type: boolean
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description: |
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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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input:
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- fasta:
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type: file
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description: |
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Input genome fasta file
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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- fasta:
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type: file
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description: Input genome fasta file
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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output:
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- index:
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type: file
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description: BWA genome index files
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pattern: "*.{fasta}.{amb,ann,bwt,pac,sa}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.version.txt"
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- index:
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type: file
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description: BWA genome index files
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pattern: "*.{amb,ann,bwt,pac,sa}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@drpatelh"
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- "@maxulysse"
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- "@drpatelh"
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- "@maxulysse"
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@ -1,20 +1,20 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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}
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profiles {
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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@ -1,68 +1,69 @@
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name: bwa_mem
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description: Performs fastq alignment to a fasta reference using BWA
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keywords:
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- mem
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- bwa
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- alignment
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- map
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- mem
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- bwa
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- alignment
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- map
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- fastq
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- bam
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- sam
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tools:
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- bwa:
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description: |
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BWA 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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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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- bwa:
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description: |
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BWA 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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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- outdir:
|
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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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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- conda:
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type: boolean
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description: |
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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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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: file
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description: |
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BWA genome index files
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pattern: "*.{amb,ann,bwt,pac,sa}"
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- fasta:
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type: file
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description: |
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Input genome fasta file
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: file
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description: BWA genome index files
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pattern: "*.{amb,ann,bwt,pac,sa}"
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- fasta:
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type: file
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description: Input genome fasta file
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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output:
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.bam"
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- version:
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type: file
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description: File containing software version
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pattern: "*.version.txt"
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@drpatelh"
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- "@jeremy1805"
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- "@drpatelh"
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- "@jeremy1805"
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|
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@ -1,20 +1,20 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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}
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profiles {
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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|
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@ -1,71 +1,72 @@
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name: fastqc
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description: Run FastQC on sequenced reads
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keywords:
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- quality control
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- qc
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- adapters
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- quality control
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- qc
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- adapters
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- fastq
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tools:
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- fastqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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- fastqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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params:
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- outdir:
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type: string
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description: |
|
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
|
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- publish_dir_mode:
|
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type: string
|
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description: |
|
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
|
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- conda:
|
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type: boolean
|
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description: |
|
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Run the module with Conda using the software specified
|
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via the `conda` directive
|
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- outdir:
|
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type: string
|
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description: |
|
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
|
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- publish_dir_mode:
|
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type: string
|
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description: |
|
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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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- conda:
|
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type: boolean
|
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description: |
|
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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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input:
|
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- meta:
|
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type: map
|
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description: |
|
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
|
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- reads:
|
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type: file
|
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description: |
|
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
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respectively.
|
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- options:
|
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type: map
|
||||
description: |
|
||||
Groovy Map containing module options for passing command-line arguments and
|
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output file paths.
|
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- meta:
|
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type: map
|
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description: |
|
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Groovy Map containing sample information
|
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e.g. [ id:'test', single_end:false ]
|
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- reads:
|
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type: file
|
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description: |
|
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- options:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing module options for passing command-line arguments and
|
||||
output file paths.
|
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output:
|
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- meta:
|
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type: map
|
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description: |
|
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Groovy Map containing sample information
|
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e.g. [ id:'test', single_end:false ]
|
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- html:
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type: file
|
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description: FastQC report
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pattern: "*_fastqc.html"
|
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- zip:
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type: file
|
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description: FastQC report archive
|
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pattern: "*_fastqc.zip"
|
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- version:
|
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type: file
|
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description: File containing software version
|
||||
pattern: "*.version.txt"
|
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- meta:
|
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type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
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e.g. [ id:'test', single_end:false ]
|
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- html:
|
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type: file
|
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description: FastQC report
|
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pattern: "*_{fastqc.html}"
|
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- zip:
|
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type: file
|
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description: FastQC report archive
|
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pattern: "*_{fastqc.zip}"
|
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- version:
|
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type: file
|
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description: File containing software version
|
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pattern: "*.{version.txt}"
|
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authors:
|
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- "@drpatelh"
|
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- "@grst"
|
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- "@ewels"
|
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- "@FelixKrueger"
|
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- "@drpatelh"
|
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- "@grst"
|
||||
- "@ewels"
|
||||
- "@FelixKrueger"
|
||||
|
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|
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|
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@ -1,20 +1,20 @@
|
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|
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params {
|
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outdir = "output/"
|
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publish_dir_mode = "copy"
|
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conda = false
|
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outdir = "output/"
|
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publish_dir_mode = "copy"
|
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conda = false
|
||||
}
|
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|
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profiles {
|
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conda {
|
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params.conda = true
|
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}
|
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docker {
|
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docker.enabled = true
|
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docker.runOptions = '-u \$(id -u):\$(id -g)'
|
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}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
conda {
|
||||
params.conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
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|
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|
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@ -1,97 +1,98 @@
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name: trimgalore
|
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description: Trim FastQ files using Trim Galore!
|
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keywords:
|
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- trimming
|
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- adapters
|
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- sequencing adapters
|
||||
- trimming
|
||||
- adapters
|
||||
- sequencing adapters
|
||||
- fastq
|
||||
tools:
|
||||
- trimgalore:
|
||||
description: |
|
||||
A wrapper tool around Cutadapt and FastQC to consistently apply quality
|
||||
and adapter trimming to FastQ files, with some extra functionality for
|
||||
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
|
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
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documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
|
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- trimgalore:
|
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description: |
|
||||
A wrapper tool around Cutadapt and FastQC to consistently apply quality
|
||||
and adapter trimming to FastQ files, with some extra functionality for
|
||||
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
|
||||
homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
||||
documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
|
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params:
|
||||
- outdir:
|
||||
type: string
|
||||
description: |
|
||||
The pipeline's output directory. By default, the module will
|
||||
output files into `$params.outdir/<SOFTWARE>`
|
||||
- publish_dir_mode:
|
||||
type: string
|
||||
description: |
|
||||
Value for the Nextflow `publishDir` mode parameter.
|
||||
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||||
- conda:
|
||||
type: boolean
|
||||
description: |
|
||||
Run the module with Conda using the software specified
|
||||
via the `conda` directive
|
||||
- clip_r1:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 5' end of read 1
|
||||
(or single-end reads)
|
||||
- clip_r2:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 5' end of read 2
|
||||
(paired-end reads only)
|
||||
- three_prime_clip_r1:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 3' end of read 1
|
||||
AFTER adapter/quality trimming has been performed
|
||||
- three_prime_clip_r2:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to re move bp from the 3' end of read 2
|
||||
AFTER adapter/quality trimming has been performed
|
||||
- outdir:
|
||||
type: string
|
||||
description: |
|
||||
The pipeline's output directory. By default, the module will
|
||||
output files into `$params.outdir/<SOFTWARE>`
|
||||
- publish_dir_mode:
|
||||
type: string
|
||||
description: |
|
||||
Value for the Nextflow `publishDir` mode parameter.
|
||||
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||||
- conda:
|
||||
type: boolean
|
||||
description: |
|
||||
Run the module with Conda using the software specified
|
||||
via the `conda` directive
|
||||
- clip_r1:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 5' end of read 1
|
||||
(or single-end reads)
|
||||
- clip_r2:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 5' end of read 2
|
||||
(paired-end reads only)
|
||||
- three_prime_clip_r1:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to remove bp from the 3' end of read 1
|
||||
AFTER adapter/quality trimming has been performed
|
||||
- three_prime_clip_r2:
|
||||
type: integer
|
||||
description: |
|
||||
Instructs Trim Galore to re move bp from the 3' end of read 2
|
||||
AFTER adapter/quality trimming has been performed
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- options:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing module options for passing command-line arguments and
|
||||
output file paths.
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- options:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing module options for passing command-line arguments and
|
||||
output file paths.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input adapter trimmed FastQ files of size 1 and 2 for
|
||||
single-end and paired-end data, respectively.
|
||||
pattern: "*.fq.gz"
|
||||
- html:
|
||||
type: file
|
||||
description: FastQC report (optional)
|
||||
pattern: "*_fastqc.html"
|
||||
- zip:
|
||||
type: file
|
||||
description: FastQC report archive (optional)
|
||||
pattern: "*_fastqc.zip"
|
||||
- log:
|
||||
type: file
|
||||
description: Trim Galore! trimming report
|
||||
pattern: "*report.txt"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.version.txt"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input adapter trimmed FastQ files of size 1 and 2 for
|
||||
single-end and paired-end data, respectively.
|
||||
pattern: "*.{fq.gz}"
|
||||
- html:
|
||||
type: file
|
||||
description: FastQC report (optional)
|
||||
pattern: "*_{fastqc.html}"
|
||||
- zip:
|
||||
type: file
|
||||
description: FastQC report archive (optional)
|
||||
pattern: "*_{fastqc.zip}"
|
||||
- log:
|
||||
type: file
|
||||
description: Trim Galore! trimming report
|
||||
pattern: "*_{report.txt}"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@ewels"
|
||||
|
|
|
|||
|
|
@ -1,25 +1,25 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
conda = false
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
conda = false
|
||||
|
||||
clip_r1 = 0
|
||||
clip_r2 = 0
|
||||
three_prime_clip_r1 = 0
|
||||
three_prime_clip_r2 = 0
|
||||
clip_r1 = 0
|
||||
clip_r2 = 0
|
||||
three_prime_clip_r1 = 0
|
||||
three_prime_clip_r2 = 0
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
conda {
|
||||
params.conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue