GitHub - aleksandrabliznina/modules: Repository to host tool-specific module files for the Nextflow DSL2 community!

THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE! PLEASE BE KIND TO OUR CODE REVIEWERS AND SUBMIT ONE PULL REQUEST PER MODULE :)

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation.

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 software/ 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.

Install the latest version of nf-core/tools (>=1.13)

List the available modules:

$ nf-core modules list

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

nf-core/tools version 1.13

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 . --tool fastqc

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

nf-core/tools version 1.13

INFO     Installing fastqc                                                      pipeline_modules.py:213
INFO     Downloaded 3 files to ./modules/nf-core/software/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/software/fastqc/main' addParams( options: [:] )

Remove the module from the pipeline repository if required:

$ nf-core modules remove . --tool fastqc

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

nf-core/tools version 1.13

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 . --tool fastqc

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

nf-core/tools version 1.13

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/software/fastqc/ │
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔]  15 Tests Passed │
│ [!]   1 Test Warning │
│ [✗]   0 Test Failed  │
╰──────────────────────╯

We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space e.g. nf-core modules update command to automatically check and update modules installed within the pipeline.

Adding a new module file

If you decide to upload a module to nf-core/modules then this will ensure that it will become available to all nf-core pipelines, and to everyone within the Nextflow community! See software/ for examples.

Checklist

Please check that the module you wish to add isn't already on nf-core/modules:

If the module doesn't exist on nf-core/modules:

Please create a new issue before adding it
Set an appropriate subject for the issue e.g. new module: fastqc
Add yourself to the Assignees so we can track who is working on the module

nf-core modules create

We have implemented a number of commands in the nf-core/tools package to make it incredibly easy for you to create and contribute your own modules to nf-core/modules.

Install the latest version of nf-core/tools (>=1.13)
Install Nextflow (>=21.04.0)
Install any of Docker, Singularity or Conda
Fork and clone this repo locally
Set up git by adding a new remote of the nf-core git repo called upstream
```
git remote add upstream https://github.com/nf-core/modules.git
```
Make a new branch for your module and check it out
```
git checkout -b fastqc
```
Create a module using the nf-core DSL2 module template:
```
$ nf-core modules create . --tool fastqc --author @joebloggs --label process_low --meta

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

nf-core/tools version 1.13

INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'                      create.py:130
INFO     Using Docker / Singularity container with tag: 'fastqc:0.11.9--0'      create.py:140
INFO     Created / edited following files:                                      create.py:218
            ./software/fastqc/functions.nf
            ./software/fastqc/main.nf
            ./software/fastqc/meta.yml
            ./tests/software/fastqc/main.nf
            ./tests/software/fastqc/test.yml
            ./tests/config/pytest_software.yml
```
All of the files required to add the module to nf-core/modules will be created/edited in the appropriate places. The 4 files you will need to change are:
1. ./software/fastqc/main.nf
  
  This is the main script containing the process definition for the module. You will see an extensive number of TODO statements to help guide you to fill in the appropriate sections and to ensure that you adhere to the guidelines we have set for module submissions.
2. ./software/fastqc/meta.yml
  
  This file will be used to store general information about the module and author details - the majority of which will already be auto-filled. However, you will need to add a brief description of the files defined in the input and output section of the main script since these will be unique to each module.
3. ./tests/software/fastqc/main.nf
  
  Every module MUST have a test workflow. This file will define one or more Nextflow workflow definitions that will be used to unit test the output files created by the module. By default, one workflow definition will be added but please feel free to add as many as possible so we can ensure that the module works on different data types / parameters e.g. separate workflow for single-end and paired-end data.
  
  Minimal test data required for your module may already exist within this repository, in which case you may just have to change a couple of paths in this file - see the Test data section for more info and guidelines for adding new standardised data if required.
4. ./tests/software/fastqc/test.yml
  
  This file will contain all of the details required to unit test the main script in the point above using pytest-workflow. If possible, any outputs produced by the test workflow(s) MUST be included and listed in this file along with an appropriate check e.g. md5sum. The different test options are listed in the pytest-workflow docs.
  
  As highlighted in the next point, we have added a command to make it much easier to test the workflow(s) defined for the module and to automatically create the test.yml with the md5sum hashes for all of the outputs generated by the module.
  
  md5sum checks are the preferable choice of test to determine file changes, however, this may not be possible for all outputs generated by some tools e.g. if they include time stamps or command-related headers. Please do your best to avoid just checking for the file being present e.g. it may still be possible to check that the file contains the appropriate text snippets.

Create a yaml file containing information required for module unit testing

$ nf-core modules create-test-yml

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

nf-core/tools version 1.13


INFO     Press enter to use default values (shown in brackets) or type your own responses                                             test_yml_builder.py:51
? Tool name: fastqc
Test YAML output path (- for stdout) (tests/software/fastqc/test.yml):
INFO     Looking for test workflow entry points: 'tests/software/fastqc/main.nf'                                                      test_yml_builder.py:116
INFO     Building test meta for entry point 'test_fastqc_single_end'                                                                  test_yml_builder.py:150
Test name (fastqc test_fastqc_single_end):
Test command (nextflow run tests/software/fastqc -entry test_fastqc_single_end -c tests/config/nextflow.config):
Test tags (comma separated) (fastqc,fastqc_single_end):
Test output folder with results (leave blank to run test):
? Choose software profile Singularity
INFO     Setting env var '$PROFILE' to 'singularity'                                                                                  test_yml_builder.py:258
INFO     Running 'fastqc' test with command:                                                                                          test_yml_builder.py:263
         nextflow run tests/software/fastqc -entry test_fastqc_single_end -c tests/config/nextflow.config --outdir /tmp/tmpgbneftf5
INFO     Test workflow finished!                                                                                                      test_yml_builder.py:276
INFO     Writing to 'tests/software/fastqc/test.yml'                                                                                  test_yml_builder.py:293

NB: See docs for running tests manually if you would like to run the tests manually.

Lint the module locally to check that it adheres to nf-core guidelines before submission

$ nf-core modules lint . --tool fastqc

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

nf-core/tools version 1.13

INFO     Linting modules repo: .                                                lint.py:102
INFO     Linting module: fastqc                                                 lint.py:106

╭────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 3 Test Warnings                                                                                            │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬──────────────────────────────────────────────────────────────┬──────────────────────────────────╮
│ Module name  │ Test message                                                 │ File path                        │
├──────────────┼──────────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ fastqc       │ TODO string in meta.yml: #Add a description of the module... │ modules/nf-core/software/fastqc/ │
│ fastqc       │ TODO string in meta.yml: #Add a description and other det... │ modules/nf-core/software/fastqc/ │
│ fastqc       │ TODO string in meta.yml: #Add a description of all of the... │ modules/nf-core/software/fastqc/ │
╰──────────────┴──────────────────────────────────────────────────────────────┴──────────────────────────────────╯
╭────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Failed                                                                                              │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬──────────────────────────────────────────────────────────────┬──────────────────────────────────╮
│ Module name  │ Test message                                                 │ File path                        │
├──────────────┼──────────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ fastqc       │ 'meta' map not emitted in output channel(s)                  │ modules/nf-core/software/fastqc/ │
╰──────────────┴──────────────────────────────────────────────────────────────┴──────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔]  38 Tests Passed │
│ [!]   3 Test Warning │
│ [✗]   1 Test Failed  │
╰──────────────────────╯

Once ready, the code can be pushed and a pull request (PR) created

On a regular basis you can pull upstream changes into this branch and it is recommended to do so before pushing and creating a pull request - see below. Rather than merging changes directly from upstream the rebase strategy is recommended so that your changes are applied on top of the latest master branch from the nf-core repo. This can be performed as follows
```
git pull --rebase upstream master
```
Once you are ready you can push the code and create a PR
```
git push -u origin fastqc
```
Once the PR has been accepted you should delete the branch and checkout master again.
```
git checkout master
git branch -d fastqc
```
In case there are commits on the local branch that didn't make it into the PR (usually commits made after the PR), git will warn about this and not delete the branch. If you are sure you want to delete, use the following command
```
git branch -D fastqc
```

Test data

In order to test that each module added to nf-core/modules is actually working and to be able to track any changes to results files between module updates we have set-up a number of Github Actions CI tests to run each module on a minimal test dataset using Docker, Singularity and Conda.

All test data for nf-core/modules MUST be added to the modules branch of nf-core/test-datasets and organised by filename extension.
In order to keep the size of this repository as minimal as possible, pre-existing files from nf-core/test-datasets MUST be reused if at all possible.
Test files MUST be kept as tiny as possible.
If the appropriate test data doesn't exist in the modules branch of nf-core/test-datasets please contact us on the nf-core Slack #modules channel (you can join with this invite) to discuss possible options.

Running tests manually

As outlined in the nf-core modules create section we have made it quite trivial to create an initial yaml file (via the nf-core modules create-test-yml command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with pytest-workflow before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the test.yml file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the pytest-workflow docs.

Please follow the steps below to run the tests locally:

Install Nextflow (>=21.04.0)
Install any of Docker, Singularity or Conda
Install pytest-workflow

Start running your own tests using the appropriate tag defined in the test.yml:

Typical command with Docker:

cd /path/to/git/clone/of/nf-core/modules/
PROFILE=docker pytest --tag fastqc --symlink --keep-workflow-wd

Typical command with Singularity:

cd /path/to/git/clone/of/nf-core/modules/
TMPDIR=~ PROFILE=singularity pytest --tag fastqc --symlink --keep-workflow-wd

Typical command with Conda:

cd /path/to/git/clone/of/nf-core/modules/
PROFILE=conda pytest --tag fastqc --symlink --keep-workflow-wd

See docs on running pytest-workflow for more info.

Uploading to `nf-core/modules`

Fork the nf-core/modules repository to your own GitHub account. Within the local clone of your fork add the module file to the software/ directory. Please try and keep PRs as atomic as possible to aid the reviewing process - ideally, one module addition/update per PR.

Commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/modules GitHub repo with the appropriate information.

We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.

Guidelines

The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119.

General

Software that can be piped together SHOULD be added to separate module files unless there is a run-time, storage advantage in implementing in this way. For example, using a combination of bwa and samtools to output a BAM file instead of a SAM file:
```
bwa mem | samtools view -B -T ref.fasta
```
Where applicable, the usage and generation of compressed files SHOULD be enforced as input and output, respectively:
- *.fastq.gz and NOT *.fastq
- *.bam and NOT *.sam
Where applicable, each module command MUST emit a file <SOFTWARE>.version.txt containing a single line with the software's version in the format <VERSION_NUMBER> or 0.7.17 e.g.
```
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
```
If the software is unable to output a version number on the command-line then a variable called VERSION can be manually specified to create this file e.g. homer/annotatepeaks module.
The process definition MUST NOT contain a when statement.

Naming conventions

The directory structure for the module name must be all lowercase e.g. software/bwa/mem/. The name of the software (i.e. bwa) and tool (i.e. mem) MUST be all one word.
The process name in the module file MUST be all uppercase e.g. process BWA_MEM {. The name of the software (i.e. BWA) and tool (i.e. MEM) MUST be all one word separated by an underscore.
All parameter names MUST follow the snake_case convention.
All function names MUST follow the camelCase convention.

Module parameters

A module file SHOULD only define input and output files as command-line parameters to be executed within the process.
All other parameters MUST be provided as a string i.e. options.args where options is a Groovy Map that MUST be provided via the Nextflow addParams option when including the module via include in the parent workflow.
If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow task variable e.g. --threads $task.cpus.
Any parameters that need to be evaluated in the context of a particular sample e.g. single-end/paired-end data MUST also be defined within the process.

Input/output options

Named file extensions MUST be emitted for ALL output channels e.g. path "*.txt", emit: txt.
Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.

Resource requirements

An appropriate resource label MUST be provided for the module as listed in the nf-core pipeline template e.g. process_low, process_medium or process_high.
If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow task variable e.g. --threads $task.cpus.

Software requirements

BioContainers is a registry of Docker and Singularity containers automatically created from all of the software packages on Bioconda. Where possible we will use BioContainers to fetch pre-built software containers and Bioconda to install software using Conda.

Software requirements SHOULD be declared within the module file using the Nextflow container directive. For single-tool BioContainers, the nf-core modules create command will automatically fetch and fill-in the appropriate Conda / Docker / Singularity definitions by parsing the information provided in the first part of the module name:

conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)                         // Conda package
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
    container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"  // Singularity image
} else {
    container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"                        // Docker image
}

If the software is available on Conda it MUST also be defined using the Nextflow conda directive. Using bioconda::bwa=0.7.17 as an example, software MUST be pinned to the channel (i.e. bioconda) and version (i.e. 0.7.17). Conda packages MUST not be pinned to a build because they can vary on different platforms.
If required, multi-tool containers may also be available on BioContainers e.g. bwa and samtools. You can install and use the galaxy-tool-util package to search for both single- and multi-tool containers available in Conda, Docker and Singularity format. e.g. to search for Docker (hosted on Quay.io) and Singularity multi-tool containers with both bowtie and samtools installed you can use the following command:
```
mulled-search --destination quay singularity --channel bioconda --search bowtie samtools | grep "mulled"
```
NB: Build information for all tools within a multi-tool container can be obtained in the /usr/local/conda-meta/history file within the container.
It is also possible for a new multi-tool container to be built and added to BioContainers by submitting a pull request on their multi-package-containers repository.
- Fork the multi-package-containers repository
- Make a change to the hash.tsv file in the combinations directory see here for an example where pysam=0.16.0.1,biopython=1.78 was added.
- Commit the code and then make a pull request to the original repo, for example
- Once the PR has been accepted a container will get built and you can find it using a search tool in the galaxy-tool-util conda package
```
mulled-search --destination quay singularity conda  --search pysam biopython  | grep "mulled"
quay         mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f  185a25ca79923df85b58f42deb48f5ac4481e91f-0  docker pull quay.io/biocontainers/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0
singularity  mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f  185a25ca79923df85b58f42deb48f5ac4481e91f-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0
```
- You can copy and paste the mulled-* path into the relevant Docker and Singularity lines in the Nextflow process definition of your module
- To confirm that this is correct. Spin up a temporary Docker container
```
docker run --rm -it quay.io/biocontainers/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0  /bin/sh
```
  And in the command prompt type
```
$ grep specs /usr/local/conda-meta/history
# update specs: ['biopython=1.78', 'pysam=0.16.0.1']
```
  The packages should reflect those added to the multi-package-containers repo hash.tsv file
If the software is not available on Bioconda a Dockerfile MUST be provided within the module directory. We will use GitHub Actions to auto-build the containers on the GitHub Packages registry.

Publishing results

The Nextflow publishDir definition is currently quite limited in terms of parameter/option evaluation. To overcome this, the publishing logic we have implemented for use with DSL2 modules attempts to minimise changing the publishDir directive (default: params.outdir) in favour of constructing and appending the appropriate output directory paths via the saveAs: statement e.g.

publishDir "${params.outdir}",
    mode: params.publish_dir_mode,
    saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

The saveFiles function can be found in the functions.nf file of utility functions that will be copied into all module directories. It uses the various publishing options specified as input to the module to construct and append the relevant output path to params.outdir.

We also use a standardised parameter called params.publish_dir_mode that can be used to alter the file publishing method (default: copy).

Terminology

The features offered by Nextflow DSL2 can be used in various ways depending on the granularity with which you would like to write pipelines. Please see the listing below for the hierarchy and associated terminology we have decided to use when referring to DSL2 components:

Module: A process that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as FastQC. At present, this repository has been created to only host atomic module files that should be added to the software/ directory along with the required documentation and tests.
Sub-workflow: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline. For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows although this may change in the future since well-written sub-workflows will be the most powerful aspect of DSL2.
Workflow: What DSL1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL1, or by using a combination of DSL2 individual modules and sub-workflows.

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.

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deprecated		deprecated
docs/images		docs/images
software		software
tests		tests
.editorconfig		.editorconfig
.gitattributes		.gitattributes
.gitignore		.gitignore
.markdownlint.yml		.markdownlint.yml
LICENSE		LICENSE
README.md		README.md

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