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* [FIX/DOC] Broken Adding modules link * Apply suggestion Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
175 lines
9.1 KiB
Markdown
175 lines
9.1 KiB
Markdown
# 
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[](https://www.nextflow.io/)
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[](https://docs.conda.io/en/latest/)
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[](https://www.docker.com/)
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[](https://sylabs.io/docs/)
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[](https://nfcore.slack.com/channels/modules)
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[](https://twitter.com/nf_core)
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[](https://www.youtube.com/c/nf-core)
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> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
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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.
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## Table of contents
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- [Using existing modules](#using-existing-modules)
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- [Adding new modules](#adding-new-modules)
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- [Help](#help)
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- [Citation](#citation)
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## Using existing modules
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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.
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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.
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1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.0`)
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2. List the available modules:
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```console
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$ nf-core modules list remote
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,--./,-.
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___ __ __ __ ___ /,-._.--~\
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`._,._,'
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nf-core/tools version 2.0
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INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
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┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
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┃ Module Name ┃
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┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
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│ bandage/image │
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│ bcftools/consensus │
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│ bcftools/filter │
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│ bcftools/isec │
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..truncated..
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```
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3. Install the module in your pipeline directory:
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```console
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$ nf-core modules install fastqc
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___ __ __ __ ___ /,-._.--~\
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`._,._,'
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nf-core/tools version 2.0
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INFO Installing fastqc pipeline_modules.py:213
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INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236
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```
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4. Import the module in your Nextflow script:
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```nextflow
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FASTQC } from './modules/nf-core/modules/fastqc/main'
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```
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5. Remove the module from the pipeline repository if required:
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```console
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$ nf-core modules remove fastqc
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`._,._,'
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nf-core/tools version 2.0
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INFO Removing fastqc pipeline_modules.py:271
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INFO Successfully removed fastqc pipeline_modules.py:285
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```
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6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
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```console
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$ nf-core modules lint fastqc
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`._,._,'
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nf-core/tools version 2.0
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INFO Linting pipeline: . lint.py:104
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INFO Linting module: fastqc lint.py:106
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╭─────────────────────────────────────────────────────────────────────────────────╮
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│ [!] 1 Test Warning │
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╰─────────────────────────────────────────────────────────────────────────────────╯
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╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
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│ Module name │ Test message │ File path │
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├──────────────┼───────────────────────────────┼──────────────────────────────────┤
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│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
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╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
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╭──────────────────────╮
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│ LINT RESULTS SUMMARY │
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├──────────────────────┤
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│ [✔] 15 Tests Passed │
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│ [!] 1 Test Warning │
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│ [✗] 0 Test Failed │
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╰──────────────────────╯
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```
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## Adding new modules
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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).
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> Please be kind to our code reviewers and submit one pull request per module :)
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## Help
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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)).
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## Citation
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If you use the module files in this repository for your analysis please you can cite the `nf-core` publication as follows:
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> **The nf-core framework for community-curated bioinformatics pipelines.**
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>
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> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
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>
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> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
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<!---
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### Offline usage
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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:
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```bash
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include /path/to/downloaded/modules/directory/
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```
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Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:
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```bash
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nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
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```
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> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
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> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
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# New test data created for the module- sequenzautils/bam2seqz
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The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input).
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-->
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