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>rpetit3-patch-1
Matthias Hörtenhuber
2 years ago
committed by
GitHub
parent
12b0bc5aa9
commit
e745e167c1
@ -1,14 +1,14 @@
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image: nfcore/gitpod:latest
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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extensions: # based on nf-core.nf-core-extensionpack
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- codezombiech.gitignore # Language support for .gitignore files
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# - cssho.vscode-svgviewer # SVG viewer
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# - cssho.vscode-svgviewer # SVG viewer
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- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
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- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
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- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
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- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
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- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
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# - nextflow.nextflow # Nextflow syntax highlighting
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# - nextflow.nextflow # Nextflow syntax highlighting
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- oderwat.indent-rainbow # Highlight indentation level
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- streetsidesoftware.code-spell-checker # Spelling checker for source code
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@ -0,0 +1,5 @@
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extends: default
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rules:
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document-start: disable
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line-length: disable
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@ -1,50 +1,50 @@
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name: adapterremoval
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description: Trim sequencing adapters and collapse overlapping reads
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keywords:
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- trimming
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- adapters
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- merging
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- fastq
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- trimming
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- adapters
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- merging
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- fastq
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tools:
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- adapterremoval:
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description: The AdapterRemoval v2 tool for merging and clipping reads.
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homepage: https://github.com/MikkelSchubert/adapterremoval
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documentation: https://adapterremoval.readthedocs.io
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licence: ['GPL v3']
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- adapterremoval:
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description: The AdapterRemoval v2 tool for merging and clipping reads.
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homepage: https://github.com/MikkelSchubert/adapterremoval
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documentation: https://adapterremoval.readthedocs.io
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licence: ["GPL v3"]
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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, collapse: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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pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
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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, collapse: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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pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
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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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- reads:
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type: file
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description: |
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List of input adapter trimmed FastQ files of size 1 or 2 for
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single-end or collapsed data and paired-end data, respectively.
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pattern: "*.{fastq.gz}"
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- log:
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type: file
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description: AdapterRemoval log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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 adapter trimmed FastQ files of size 1 or 2 for
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single-end or collapsed data and paired-end data, respectively.
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pattern: "*.{fastq.gz}"
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- log:
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type: file
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description: AdapterRemoval log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@maxibor"
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- "@maxibor"
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@ -1,44 +1,44 @@
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name: bandage_image
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description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
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keywords:
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- gfa
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- graph
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- assembly
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- visualisation
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- gfa
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- graph
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- assembly
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- visualisation
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tools:
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- bandage:
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description: |
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Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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homepage: https://github.com/rrwick/Bandage
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documentation: https://github.com/rrwick/Bandage
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licence: ['GPL-3.0-or-later']
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- bandage:
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description: |
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Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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homepage: https://github.com/rrwick/Bandage
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documentation: https://github.com/rrwick/Bandage
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licence: ["GPL-3.0-or-later"]
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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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- gfa:
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type: file
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description: Assembly graph in GFA 1.0 format
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pattern: "*.gfa"
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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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- gfa:
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type: file
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description: Assembly graph in GFA 1.0 format
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pattern: "*.gfa"
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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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- png:
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type: file
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description: Bandage image in PNG format
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pattern: "*.png"
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- svg:
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type: file
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description: Bandage image in SVG format
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pattern: "*.svg"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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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- png:
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type: file
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description: Bandage image in PNG format
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pattern: "*.png"
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- svg:
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type: file
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description: Bandage image in SVG format
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pattern: "*.svg"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@heuermh"
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- "@heuermh"
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@ -1,43 +1,43 @@
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name: bcftools_concat
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description: Concatenate VCF files
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keywords:
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- variant calling
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- concat
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- bcftools
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- VCF
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- variant calling
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- concat
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- bcftools
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- VCF
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tools:
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- concat:
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description: |
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Concatenate VCF files.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ['MIT']
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- concat:
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description: |
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Concatenate VCF files.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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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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- vcfs:
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type: files
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description: |
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List containing 2 or more vcf files
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e.g. [ 'file1.vcf', 'file2.vcf' ]
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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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- vcfs:
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type: files
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description: |
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List containing 2 or more vcf files
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e.g. [ 'file1.vcf', 'file2.vcf' ]
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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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- vcf:
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type: file
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description: VCF concatenated output file
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pattern: "*.{vcf.gz}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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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- vcf:
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type: file
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description: VCF concatenated output file
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pattern: "*.{vcf.gz}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@abhi18av"
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@ -1,49 +1,49 @@
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name: bcftools_consensus
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description: Compresses VCF files
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keywords:
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- variant calling
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- consensus
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- VCF
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- variant calling
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- consensus
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- VCF
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tools:
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- consensus:
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description: |
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Create consensus sequence by applying VCF variants to a reference fasta file.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ['MIT']
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- consensus:
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description: |
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Create consensus sequence by applying VCF variants to a reference fasta file.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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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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- vcf:
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type: file
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description: VCF file
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pattern: "*.{vcf}"
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- tbi:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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- meta:
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type: map
|
||||
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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- vcf:
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type: file
|
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description: VCF file
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pattern: "*.{vcf}"
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- tbi:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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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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- fasta:
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type: file
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description: FASTA reference consensus file
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pattern: "*.{fasta,fa}"
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- versions:
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type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
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- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
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e.g. [ id:'test', single_end:false ]
|
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- fasta:
|
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type: file
|
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description: FASTA reference consensus file
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pattern: "*.{fasta,fa}"
|
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- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
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@ -1,41 +1,41 @@
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name: bcftools_filter
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description: Filters VCF files
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keywords:
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- variant calling
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- filtering
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- VCF
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- variant calling
|
||||
- filtering
|
||||
- VCF
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tools:
|
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- filter:
|
||||
description: |
|
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Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
|
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licence: ['MIT']
|
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- filter:
|
||||
description: |
|
||||
Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,49 +1,49 @@
|
||||
name: bcftools_isec
|
||||
description: Apply set operations to VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
tools:
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,47 +1,47 @@
|
||||
name: bcftools_merge
|
||||
description: Merge VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
tools:
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,57 +1,57 @@
|
||||
name: bcftools_mpileup
|
||||
description: Compresses VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
tools:
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,42 +1,42 @@
|
||||
name: bcftools_stats
|
||||
description: Generates stats from VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- stats
|
||||
- VCF
|
||||
- variant calling
|
||||
- stats
|
||||
- VCF
|
||||
tools:
|
||||
- stats:
|
||||
description: |
|
||||
Parses VCF or BCF and produces text file stats which is suitable for
|
||||
machine processing and can be plotted using plot-vcfstats.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- stats:
|
||||
description: |
|
||||
Parses VCF or BCF and produces text file stats which is suitable for
|
||||
machine processing and can be plotted using plot-vcfstats.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*_{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*_{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,63 +1,63 @@
|
||||
name: bcftools_view
|
||||
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
keywords:
|
||||
- variant calling
|
||||
- view
|
||||
- bcftools
|
||||
- VCF
|
||||
- variant calling
|
||||
- view
|
||||
- bcftools
|
||||
- VCF
|
||||
|
||||
tools:
|
||||
- view:
|
||||
description: |
|
||||
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- view:
|
||||
description: |
|
||||
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be inspected.
|
||||
e.g. 'file.vcf'
|
||||
- index:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
e.g. 'file.tbi'
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
e.g. 'file.vcf'
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
e.g. 'file.vcf'
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be inspected.
|
||||
e.g. 'file.vcf'
|
||||
- index:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
e.g. 'file.tbi'
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
e.g. 'file.vcf'
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
e.g. 'file.vcf'
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@abhi18av"
|
||||
|
||||
@ -1,38 +1,38 @@
|
||||
name: bedtools_bamtobed
|
||||
description: Converts a bam file to a bed12 file.
|
||||
keywords:
|
||||
- bam
|
||||
- bed
|
||||
- bam
|
||||
- bed
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file containing genomic intervals.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file containing genomic intervals.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,43 +1,43 @@
|
||||
name: bedtools_complement
|
||||
description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
|
||||
keywords:
|
||||
- bed
|
||||
- complement
|
||||
- bed
|
||||
- complement
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- sizes:
|
||||
type: file
|
||||
description: File which defines the chromosome lengths for a given genome
|
||||
pattern: "*.{sizes}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- sizes:
|
||||
type: file
|
||||
description: File which defines the chromosome lengths for a given genome
|
||||
pattern: "*.{sizes}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,51 +1,51 @@
|
||||
name: bedtools_genomecov
|
||||
description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
|
||||
keywords:
|
||||
- bed
|
||||
- bam
|
||||
- genomecov
|
||||
- bed
|
||||
- bam
|
||||
- genomecov
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- scale:
|
||||
type: value
|
||||
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
|
||||
- sizes:
|
||||
type: file
|
||||
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- scale:
|
||||
type: value
|
||||
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
|
||||
- sizes:
|
||||
type: file
|
||||
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- genomecov:
|
||||
type: file
|
||||
description: Computed genome coverage file
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- genomecov:
|
||||
type: file
|
||||
description: Computed genome coverage file
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@chris-cheshire"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@chris-cheshire"
|
||||
|
||||
@ -1,34 +1,34 @@
|
||||
name: bedtools_getfasta
|
||||
description: extract sequences in a FASTA file based on intervals defined in a feature file.
|
||||
keywords:
|
||||
- bed
|
||||
- fasta
|
||||
- getfasta
|
||||
- bed
|
||||
- fasta
|
||||
- getfasta
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
output:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output fasta file with extracted sequences
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output fasta file with extracted sequences
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,47 +1,47 @@
|
||||
name: bedtools_intersect
|
||||
description: Allows one to screen for overlaps between two sets of genomic features.
|
||||
keywords:
|
||||
- bed
|
||||
- intersect
|
||||
- bed
|
||||
- intersect
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals1:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- intervals2:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- extension:
|
||||
type: value
|
||||
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals1:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- intervals2:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- extension:
|
||||
type: value
|
||||
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intersect:
|
||||
type: file
|
||||
description: File containing the description of overlaps found between the two features
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intersect:
|
||||
type: file
|
||||
description: File containing the description of overlaps found between the two features
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
|
||||
@ -1,44 +1,44 @@
|
||||
name: bedtools_maskfasta
|
||||
description: masks sequences in a FASTA file based on intervals defined in a feature file.
|
||||
keywords:
|
||||
- bed
|
||||
- fasta
|
||||
- maskfasta
|
||||
- bed
|
||||
- fasta
|
||||
- maskfasta
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output masked fasta file
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output masked fasta file
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,39 +1,39 @@
|
||||
name: bedtools_merge
|
||||
description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
|
||||
keywords:
|
||||
- bed
|
||||
- merge
|
||||
- bed
|
||||
- merge
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Overlapped bed file with combined features
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Overlapped bed file with combined features
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,39 +1,39 @@
|
||||
name: bedtools_slop
|
||||
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
|
||||
keywords:
|
||||
- bed
|
||||
- slopBed
|
||||
- bed
|
||||
- slopBed
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Slopped BED file
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Slopped BED file
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,46 +1,46 @@
|
||||
name: bedtools_sort
|
||||
description: Sorts a feature file by chromosome and other criteria.
|
||||
keywords:
|
||||
- bed
|
||||
- sort
|
||||
- bed
|
||||
- sort
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BED/BEDGRAPH
|
||||
pattern: "*.{bed|bedGraph}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BED/BEDGRAPH
|
||||
pattern: "*.{bed|bedGraph}"
|
||||
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
|
||||
- sorted:
|
||||
type: file
|
||||
description: Sorted output file
|
||||
pattern: "*.${extension}"
|
||||
- sorted:
|
||||
type: file
|
||||
description: Sorted output file
|
||||
pattern: "*.${extension}"
|
||||
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@chris-cheshire"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@chris-cheshire"
|
||||
|
||||
@ -1,44 +1,44 @@
|
||||
name: biobambam_bammarkduplicates2
|
||||
description: Locate and tag duplicate reads in a BAM file
|
||||
keywords:
|
||||
- markduplicates
|
||||
- bam
|
||||
- cram
|
||||
- markduplicates
|
||||
- bam
|
||||
- cram
|
||||
tools:
|
||||
- biobambam:
|
||||
description: |
|
||||
biobambam is a set of tools for early stage alignment file processing.
|
||||
homepage: https://gitlab.com/german.tischler/biobambam2
|
||||
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
|
||||
doi: 10.1186/1751-0473-9-13
|
||||
licence: ['GPL v3']
|
||||
- biobambam:
|
||||
description: |
|
||||
biobambam is a set of tools for early stage alignment file processing.
|
||||
homepage: https://gitlab.com/german.tischler/biobambam2
|
||||
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
|
||||
doi: 10.1186/1751-0473-9-13
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/CRAM file
|
||||
pattern: "*.{bam,cram}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/CRAM file
|
||||
pattern: "*.{bam,cram}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file with duplicate reads marked/removed
|
||||
pattern: "*.{bam}"
|
||||
- metrics:
|
||||
type: file
|
||||
description: Duplicate metrics file generated by biobambam
|
||||
pattern: "*.{metrics.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file with duplicate reads marked/removed
|
||||
pattern: "*.{bam}"
|
||||
- metrics:
|
||||
type: file
|
||||
description: Duplicate metrics file generated by biobambam
|
||||
pattern: "*.{metrics.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@muffato"
|
||||
- "@muffato"
|
||||
|
||||
@ -1,59 +1,59 @@
|
||||
name: bismark_align
|
||||
description: Performs alignment of BS-Seq reads using bismark
|
||||
keywords:
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
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']
|
||||
- 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:
|
||||
- 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.
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- 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.
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- unmapped:
|
||||
type: file
|
||||
description: Output FastQ file(s) containing unmapped reads
|
||||
pattern: "*.{fq.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- unmapped:
|
||||
type: file
|
||||
description: Output FastQ file(s) containing unmapped reads
|
||||
pattern: "*.{fq.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,52 +1,52 @@
|
||||
name: bismark_deduplicate
|
||||
description: |
|
||||
Removes alignments to the same position in the genome
|
||||
from the Bismark mapping output.
|
||||
Removes alignments to the same position in the genome
|
||||
from the Bismark mapping output.
|
||||
keywords:
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
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']
|
||||
- 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:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Deduplicated output BAM file containing read alignments
|
||||
pattern: "*.{deduplicated.bam}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Deduplicated output BAM file containing read alignments
|
||||
pattern: "*.{deduplicated.bam}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,37 +1,37 @@
|
||||
name: bismark_genomepreparation
|
||||
description: |
|
||||
Converts a specified reference genome into two different bisulfite
|
||||
converted versions and indexes them for alignments.
|
||||
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
|
||||
- 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']
|
||||
- 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
|
||||
- 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"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,67 +1,67 @@
|
||||
name: bismark_methylationextractor
|
||||
description: Extracts methylation information for individual cytosines from alignments.
|
||||
keywords:
|
||||
- bismark
|
||||
- consensus
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bedGraph
|
||||
- bismark
|
||||
- consensus
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bedGraph
|
||||
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']
|
||||
- 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:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bismark output file containing coverage and methylation metrics
|
||||
pattern: "*.{bedGraph.gz}"
|
||||
- methylation_calls:
|
||||
type: file
|
||||
description: Bismark output file containing strand-specific methylation calls
|
||||
pattern: "*.{txt.gz}"
|
||||
- coverage:
|
||||
type: file
|
||||
description: Bismark output file containing coverage metrics
|
||||
pattern: "*.{cov.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*_{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{M-bias.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bismark output file containing coverage and methylation metrics
|
||||
pattern: "*.{bedGraph.gz}"
|
||||
- methylation_calls:
|
||||
type: file
|
||||
description: Bismark output file containing strand-specific methylation calls
|
||||
pattern: "*.{txt.gz}"
|
||||
- coverage:
|
||||
type: file
|
||||
description: Bismark output file containing coverage metrics
|
||||
pattern: "*.{cov.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*_{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{M-bias.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,60 +1,60 @@
|
||||
name: bismark_report
|
||||
description: Collects bismark alignment reports
|
||||
keywords:
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
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']
|
||||
- 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:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark reports
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark reports
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,54 +1,54 @@
|
||||
name: bismark_summary
|
||||
description: |
|
||||
Uses Bismark report files of several samples in a run folder
|
||||
to generate a graphical summary HTML report.
|
||||
Uses Bismark report files of several samples in a run folder
|
||||
to generate a graphical summary HTML report.
|
||||
keywords:
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- summary
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- summary
|
||||
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']
|
||||
- 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:
|
||||
- bam:
|
||||
type: file
|
||||
description: Bismark alignment
|
||||
pattern: "*.{bam}"
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- bam:
|
||||
type: file
|
||||
description: Bismark alignment
|
||||
pattern: "*.{bam}"
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
output:
|
||||
- summary:
|
||||
type: file
|
||||
description: Bismark summary
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- summary:
|
||||
type: file
|
||||
description: Bismark summary
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,41 +1,41 @@
|
||||
name: blast_blastn
|
||||
description: Queries a BLAST DNA database
|
||||
keywords:
|
||||
- fasta
|
||||
- blast
|
||||
- blastn
|
||||
- DNA sequence
|
||||
- fasta
|
||||
- blast
|
||||
- blastn
|
||||
- DNA sequence
|
||||
tools:
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ['US-Government-Work']
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ["US-Government-Work"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file containing queries sequences
|
||||
pattern: "*.{fa,fasta}"
|
||||
- db:
|
||||
type: directory
|
||||
description: Directory containing blast database
|
||||
pattern: "*"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file containing queries sequences
|
||||
pattern: "*.{fa,fasta}"
|
||||
- db:
|
||||
type: directory
|
||||
description: Directory containing blast database
|
||||
pattern: "*"
|
||||
output:
|
||||
- txt:
|
||||
type: file
|
||||
description: File containing blastn hits
|
||||
pattern: "*.{blastn.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: File containing blastn hits
|
||||
pattern: "*.{blastn.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,31 +1,31 @@
|
||||
name: blast_makeblastdb
|
||||
description: Builds a BLAST database
|
||||
keywords:
|
||||
- fasta
|
||||
- blast
|
||||
- database
|
||||
- fasta
|
||||
- blast
|
||||
- database
|
||||
tools:
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ['US-Government-Work']
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ["US-Government-Work"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
output:
|
||||
- db:
|
||||
type: directory
|
||||
description: Output directory containing blast database files
|
||||
pattern: "*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- db:
|
||||
type: directory
|
||||
description: Output directory containing blast database files
|
||||
pattern: "*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,46 +1,46 @@
|
||||
name: bowtie_align
|
||||
description: Align reads to a reference genome using bowtie
|
||||
keywords:
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- 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
|
||||
licence: ['Artistic-2.0']
|
||||
- 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
|
||||
licence: ["Artistic-2.0"]
|
||||
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.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- 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.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
authors:
|
||||
- "@kevinmenden"
|
||||
- "@kevinmenden"
|
||||
|
||||
@ -1,32 +1,32 @@
|
||||
name: bowtie_build
|
||||
description: Create bowtie index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- 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
|
||||
licence: ['Artistic-2.0']
|
||||
- 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
|
||||
licence: ["Artistic-2.0"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@kevinmenden"
|
||||
- "@drpatelh"
|
||||
- "@kevinmenden"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,51 +1,51 @@
|
||||
name: bowtie2_align
|
||||
description: Align reads to a reference genome using bowtie2
|
||||
keywords:
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
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.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
- 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.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Aligment log
|
||||
pattern: "*.log"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Aligment log
|
||||
pattern: "*.log"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,33 +1,33 @@
|
||||
name: bowtie2_build
|
||||
description: Builds bowtie index for reference genome
|
||||
keywords:
|
||||
- build
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- build
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.bt2"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.bt2"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,32 +1,32 @@
|
||||
name: bwa_index
|
||||
description: Create BWA index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@maxulysse"
|
||||
- "@drpatelh"
|
||||
- "@maxulysse"
|
||||
|
||||
@ -1,50 +1,50 @@
|
||||
name: bwa_mem
|
||||
description: Performs fastq alignment to a fasta reference using BWA
|
||||
keywords:
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
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.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
- 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.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@jeremy1805"
|
||||
- "@drpatelh"
|
||||
- "@jeremy1805"
|
||||
|
||||
@ -1,30 +1,30 @@
|
||||
name: bwamem2_index
|
||||
description: Create BWA-mem2 index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
|
||||
licence: ['MIT']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@maxulysse"
|
||||
- "@maxulysse"
|
||||
|
||||
@ -1,49 +1,49 @@
|
||||
name: bwamem2_mem
|
||||
description: Performs fastq alignment to a fasta reference using BWA
|
||||
keywords:
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['MIT']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["MIT"]
|
||||
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.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
- 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.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@maxulysse"
|
||||
- "@maxulysse"
|
||||
|
||||
@ -1,52 +1,52 @@
|
||||
name: bwameth_align
|
||||
description: Performs alignment of BS-Seq reads using bwameth
|
||||
keywords:
|
||||
- bwameth
|
||||
- alignment
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fastq
|
||||
- bam
|
||||
- bwameth
|
||||
- alignment
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fastq
|
||||
- bam
|
||||
tools:
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ['MIT']
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ["MIT"]
|
||||
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.
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
- 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.
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,33 +1,33 @@
|
||||
name: bwameth_index
|
||||
description: Performs indexing of c2t converted reference genome
|
||||
keywords:
|
||||
- bwameth
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
- bwameth
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
tools:
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ['MIT']
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
pattern: "index"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
pattern: "index"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
||||
@ -1,39 +1,39 @@
|
||||
name: cat_fastq
|
||||
description: Concatenates fastq files
|
||||
keywords:
|
||||
- fastq
|
||||
- concatenate
|
||||
- fastq
|
||||
- concatenate
|
||||
tools:
|
||||
- cat:
|
||||
description: |
|
||||
The cat utility reads files sequentially, writing them to the standard output.
|
||||
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- cat:
|
||||
description: |
|
||||
The cat utility reads files sequentially, writing them to the standard output.
|
||||
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: list
|
||||
description: |
|
||||
List of input FastQ files to be concatenated.
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: list
|
||||
description: |
|
||||
List of input FastQ files to be concatenated.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Merged fastq file
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Merged fastq file
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
name: cellranger_count
|
||||
description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
|
||||
keywords:
|
||||
- align
|
||||
- count
|
||||
- reference
|
||||
- align
|
||||
- count
|
||||
- reference
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
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.
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- 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.
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
output:
|
||||
- outs:
|
||||
type: file
|
||||
description: Files containing the outputs of Cell Ranger
|
||||
pattern: "sample-${meta.gem}/outs/*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- outs:
|
||||
type: file
|
||||
description: Files containing the outputs of Cell Ranger
|
||||
pattern: "sample-${meta.gem}/outs/*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
- "@Emiller88"
|
||||
|
||||
@ -1,31 +1,31 @@
|
||||
name: cellranger_mkgtf
|
||||
description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
|
||||
keywords:
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- gtf:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.gtf"
|
||||
- gtf:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.gtf"
|
||||
output:
|
||||
- gtf:
|
||||
type: folder
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.filtered.gtf"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- gtf:
|
||||
type: folder
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.filtered.gtf"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
- "@Emiller88"
|
||||
|
||||
@ -1,37 +1,37 @@
|
||||
name: cellranger_mkref
|
||||
description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
|
||||
keywords:
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: fasta genome file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- gtf:
|
||||
type: file
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.gtf"
|
||||
- reference_name:
|
||||
type: val
|
||||
description: name to give the reference folder
|
||||
pattern: str
|
||||
- fasta:
|
||||
type: file
|
||||
description: fasta genome file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- gtf:
|
||||
type: file
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.gtf"
|
||||
- reference_name:
|
||||
type: val
|
||||
description: name to give the reference folder
|
||||
pattern: str
|
||||
output:
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue