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Maxime Borry 24707f2144
Fix read indexing in AdapterRemoval module (#1051)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* fix read index

* update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 12:21:12 +00:00
.github Fix workflow (#817) 2021-10-12 11:58:19 +01:00
docs/images feat: remove social preview image to use GitHub OpenGraph (#461) 2021-04-26 11:59:12 +01:00
modules Fix read indexing in AdapterRemoval module (#1051) 2021-11-10 12:21:12 +00:00
subworkflows/nf-core Add panel of normals subworkflow (#1044) 2021-11-09 10:16:43 +00:00
tests Fix read indexing in AdapterRemoval module (#1051) 2021-11-10 12:21:12 +00:00
.editorconfig Update .editorconfig 2020-06-15 16:47:42 +02:00
.gitattributes Fill out repo 2019-07-26 10:19:07 +01:00
.gitignore New module: isoseq3/cluster (#801) 2021-10-07 10:06:02 +01:00
.markdownlint.yml Update .markdownlint.yml 2021-02-17 01:15:21 +01:00
.nf-core.yml Add module: bamaligncleaner (#676) 2021-09-15 10:31:49 +02:00
LICENSE Fill out repo 2019-07-26 10:19:07 +01:00
README.md Typo fix 2021-09-20 13:00:11 +02:00

nf-core/modules

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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 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.

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

  2. 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..
    
  3. 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
    
  4. Import the module in your Nextflow script:

    #!/usr/bin/env nextflow
    
    nextflow.enable.dsl = 2
    
    include { FASTQC } from './modules/nf-core/modules/fastqc/main' addParams( options: [:] )
    
  5. 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
    
  6. 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:

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.