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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 fastqc, bwa, samtools etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
We have written 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 list remote ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.0 INFO Modules available from nf-core/modules (master): pipeline_modules.py:164 ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Module Name ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ bandage/image │ │ bcftools/consensus │ │ bcftools/filter │ │ bcftools/isec │ ..truncated.. -
Install the module in your pipeline directory:
$ nf-core modules install fastqc ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.0 INFO Installing fastqc pipeline_modules.py:213 INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236 -
Import the module in your Nextflow script:
#!/usr/bin/env nextflow nextflow.enable.dsl = 2 include { FASTQC } from './modules/nf-core/modules/fastqc/main' -
Remove the module from the pipeline repository if required:
$ nf-core modules remove fastqc ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.0 INFO Removing fastqc pipeline_modules.py:271 INFO Successfully removed fastqc pipeline_modules.py:285 -
Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
$ nf-core modules lint fastqc ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.0 INFO Linting pipeline: . lint.py:104 INFO Linting module: fastqc lint.py:106 ╭─────────────────────────────────────────────────────────────────────────────────╮ │ [!] 1 Test Warning │ ╰─────────────────────────────────────────────────────────────────────────────────╯ ╭──────────────┬───────────────────────────────┬──────────────────────────────────╮ │ Module name │ Test message │ File path │ ├──────────────┼───────────────────────────────┼──────────────────────────────────┤ │ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │ ╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯ ╭──────────────────────╮ │ LINT RESULTS SUMMARY │ ├──────────────────────┤ │ [✔] 15 Tests Passed │ │ [!] 1 Test Warning │ │ [✗] 0 Test Failed │ ╰──────────────────────╯
Adding new modules
If you wish to contribute a new module, please see the documentation on the nf-core 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 #modules channel (you can join with this invite).
Citation
If you use the module files in this repository for your analysis please you can cite the nf-core publication as follows:
<!--- ### Offline usage If you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information: ```bash include /path/to/downloaded/modules/directory/ ``` Then you can run the pipeline by directly passing the additional config file with the `-c` parameter: ```bash nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf ``` > Note that the nf-core/tools helper package has a `download` command to download all required pipeline > files + singularity containers + institutional configs + modules in one go for you, to make this process easier. # New test data created for the module- sequenzautils/bam2seqz The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input). -->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.