base on Repository to host tool-specific module files for the Nextflow DSL2 community! #  [](https://www.nextflow.io/) [](https://docs.conda.io/en/latest/) [](https://www.docker.com/) [](https://sylabs.io/docs/) <!--  --> [](https://nfcore.slack.com/channels/modules) [](https://bsky.app/profile/nf-co.re) [](https://mstdn.science/@nf_core) [](https://www.youtube.com/c/nf-core) A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation. ## Table of contents - [Using existing modules](#using-existing-modules) - [Adding new modules](#adding-new-modules) - [Help](#help) - [Citation](#citation) ## 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/`](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`](https://github.com/nf-core/tools#installation) (`>=2.0`) 2. List the available modules: ```console $ 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.. ``` 3. Install the module in your pipeline directory: ```console $ 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 ``` 4. Import the module in your Nextflow script: ```nextflow #!/usr/bin/env nextflow nextflow.enable.dsl = 2 include { FASTQC } from './modules/nf-core/modules/fastqc/main' ``` 5. Remove the module from the pipeline repository if required: ```console $ 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 ``` 6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo: ```console $ 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](https://nf-co.re/developers/modules#writing-a-new-module-reference). > 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](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)). ## 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](https://dx.doi.org/10.1038/s41587-020-0439-x). <!--- ### 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). --> ", Assign "at most 3 tags" to the expected json: {"id":"8683","tags":[]} "only from the tags list I provide: [{"id":77,"name":"3d"},{"id":89,"name":"agent"},{"id":17,"name":"ai"},{"id":54,"name":"algorithm"},{"id":24,"name":"api"},{"id":44,"name":"authentication"},{"id":3,"name":"aws"},{"id":27,"name":"backend"},{"id":60,"name":"benchmark"},{"id":72,"name":"best-practices"},{"id":39,"name":"bitcoin"},{"id":37,"name":"blockchain"},{"id":1,"name":"blog"},{"id":45,"name":"bundler"},{"id":58,"name":"cache"},{"id":21,"name":"chat"},{"id":49,"name":"cicd"},{"id":4,"name":"cli"},{"id":64,"name":"cloud-native"},{"id":48,"name":"cms"},{"id":61,"name":"compiler"},{"id":68,"name":"containerization"},{"id":92,"name":"crm"},{"id":34,"name":"data"},{"id":47,"name":"database"},{"id":8,"name":"declarative-gui "},{"id":9,"name":"deploy-tool"},{"id":53,"name":"desktop-app"},{"id":6,"name":"dev-exp-lib"},{"id":59,"name":"dev-tool"},{"id":13,"name":"ecommerce"},{"id":26,"name":"editor"},{"id":66,"name":"emulator"},{"id":62,"name":"filesystem"},{"id":80,"name":"finance"},{"id":15,"name":"firmware"},{"id":73,"name":"for-fun"},{"id":2,"name":"framework"},{"id":11,"name":"frontend"},{"id":22,"name":"game"},{"id":81,"name":"game-engine "},{"id":23,"name":"graphql"},{"id":84,"name":"gui"},{"id":91,"name":"http"},{"id":5,"name":"http-client"},{"id":51,"name":"iac"},{"id":30,"name":"ide"},{"id":78,"name":"iot"},{"id":40,"name":"json"},{"id":83,"name":"julian"},{"id":38,"name":"k8s"},{"id":31,"name":"language"},{"id":10,"name":"learning-resource"},{"id":33,"name":"lib"},{"id":41,"name":"linter"},{"id":28,"name":"lms"},{"id":16,"name":"logging"},{"id":76,"name":"low-code"},{"id":90,"name":"message-queue"},{"id":42,"name":"mobile-app"},{"id":18,"name":"monitoring"},{"id":36,"name":"networking"},{"id":7,"name":"node-version"},{"id":55,"name":"nosql"},{"id":57,"name":"observability"},{"id":46,"name":"orm"},{"id":52,"name":"os"},{"id":14,"name":"parser"},{"id":74,"name":"react"},{"id":82,"name":"real-time"},{"id":56,"name":"robot"},{"id":65,"name":"runtime"},{"id":32,"name":"sdk"},{"id":71,"name":"search"},{"id":63,"name":"secrets"},{"id":25,"name":"security"},{"id":85,"name":"server"},{"id":86,"name":"serverless"},{"id":70,"name":"storage"},{"id":75,"name":"system-design"},{"id":79,"name":"terminal"},{"id":29,"name":"testing"},{"id":12,"name":"ui"},{"id":50,"name":"ux"},{"id":88,"name":"video"},{"id":20,"name":"web-app"},{"id":35,"name":"web-server"},{"id":43,"name":"webassembly"},{"id":69,"name":"workflow"},{"id":87,"name":"yaml"}]" returns me the "expected json"