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mskcc-omics-workflows / modules

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation for MSKCC
https://mskcc-omics-workflows.gitbook.io/omics-workflows
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mskcc nextfl nextflow-dsl2 nf-core omics

readme

mskcc-omics-workflows/modules

adapted from nf-core/modules/README.md

Nextflow run with conda run with docker run with singularity

GitHub Actions Coda Linting

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.

Table of contents

Using existing modules

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.

  1. Install the latest version of nf-core/tools (>=2.0)

  2. List the available modules:

    $ nf-core modules --git-remote git@github.com:mskcc-omics-workflows/modules.git list remote

                                     ,--./,-.
     ___     __   __   __   ___     /,-._.--~\
|\ | |__  __ /  ` /  \ |__) |__         }  {
| \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                     `._,._,'

nf-core/tools version 2.14.1 - https://nf-co.re

INFO     Modules available from git@github.com:mskcc-omics-workflows/modules.git (main):

┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name                    ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ custom/splitfastqbylane        │
│ facets                         │
│ gatk4/applybqsr                │
│ gbcms                          │
..truncated..

  3. Install the module in your pipeline directory:

    $ nf-core modules --git-remote git@github.com: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'

  4. Import the module in your Nextflow script:

    #!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { FACETS } from '../modules/msk/facets/main'

  5. Remove the module from the pipeline repository if required:

    $ nf-core modules --git-remote git@github.com: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'.

  6. 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 git@github.com: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  │

Adding new modules

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 :)

Help

For further information or help, don't hesitate to get in touch on Slack #mskcc-omics-workflows channel.

Citation

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.