adapted from nf-core/modules/README.md
THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation.
The module files hosted in this repository define a set of processes for software tools such as facets, gbcms, snppileup etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
We use a helper command in the nf-core/tools package that uses the GitHub API to obtain the relevant information for the module files present in the modules/ directory of this repository. This includes using git commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.
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Install the latest version of
nf-core/tools(>=2.0) -
List the available modules:
$ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git list remote ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.14.1 - https://nf-co.re INFO Modules available from [email protected]:mskcc-omics-workflows/modules.git (main): ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Module Name ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ custom/splitfastqbylane │ │ facets │ │ gatk4/applybqsr │ │ gbcms │ ..truncated..
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Install the module in your pipeline directory:
$ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git install facets ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.14.1 - https://nf-co.re INFO Installing 'facets' INFO Use the following statement to include this module: include { FACETS } from '../modules/msk/facets/main'
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Import the module in your Nextflow script:
#!/usr/bin/env nextflow nextflow.enable.dsl = 2 include { FACETS } from '../modules/msk/facets/main'
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Remove the module from the pipeline repository if required:
$ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git remove facets ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.14.1 - https://nf-co.re INFO Removed files for 'facets' and its dependencies 'facets'.
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Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
$ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git lint facets ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.14.1 - https://nf-co.re INFO Linting pipeline: '.' INFO Linting module: 'facets' ╭─ [!] 6 Module Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Module name │ File path │ Test message │ │╶─────────────┼─────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│ │ facets │ modules/msk/facets/main.nf │ Unable to connect to container registry, code: 403, url: <https://www.docker.com/mskcc/facets-suite:2.0.9> │ │ facets │ modules/msk/facets/main.nf │ Container versions do not match │ │ facets │ modules/msk/facets/meta.yml │ hisens_r_data is present as an output in the main.nf, but missing in meta.yml │ │ facets │ modules/msk/facets/meta.yml │ purity_r_data is present as an output in the main.nf, but missing in meta.yml │ │ facets │ modules/msk/facets/meta.yml │ hisens_rdata is present as an output in meta.yml but not in main.nf │ │ facets │ modules/msk/facets/meta.yml │ purity_rdata is present as an output in meta.yml but not in main.nf │ │ ╵ ╵ │ ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ╭───────────────────────╮ │ LINT RESULTS SUMMARY │ ├───────────────────────┤ │ [✔] 59 Tests Passed │ │ [!] 6 Test Warnings │ │ [✗] 0 Tests Failed │
If you wish to contribute a new module, please see the documentation on the MSK Omics Workflow website.
Please be kind to our code reviewers and submit one pull request per module :)
For further information or help, don't hesitate to get in touch on Slack #mskcc-omics-workflows channel.
If you use the module files in this repository for your analysis please you can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.