CONTRIBUTING.md

nf-core/eager: Contributing Guidelines

Hi there! Many thanks for taking an interest in improving nf-core/eager.

We try to manage the required tasks for nf-core/eager using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time.

However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)

If you need help using or modifying nf-core/eager then the best place to ask is on the nf-core Slack #eager channel (join our Slack here).

Contribution workflow

If you'd like to write some code for nf-core/eager, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the nf-core/eager issues to avoid duplicating work
   • If there isn't one already, please create one so that others know you're working on this
2. Fork the nf-core/eager repository to your GitHub account
3. Make the necessary changes / additions within your forked repository following Pipeline conventions
4. Use nf-core schema build . and add any new parameters to the pipeline JSON schema (requires nf-core tools >= 1.10).
5. Submit a Pull Request against the dev branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

Tests

When you create a pull request with changes, GitHub Actions will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

There are typically two types of tests that run:

Lint tests

nf-core has a set of guidelines which all pipelines must adhere to. To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the nf-core/tools repository and once installed can be run locally with the nf-core lint <pipeline-directory> command.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

Pipeline tests

Each nf-core pipeline should be set up with a minimal set of test-data. GitHub Actions then runs the pipeline on this data to ensure that it exits successfully. If there are any failures then the automated tests fail. These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.

Patch

⚠️ Only in the unlikely and regretful event of a release happening with a bug.

• On your own fork, make a new branch patch based on upstream/master.
• Fix the bug, and bump version (X.Y.Z+1).
• A PR should be made on master from patch to directly this particular bug.

Getting help

For further information/help, please consult the nf-core/eager documentation and don't hesitate to get in touch on the nf-core Slack #eager channel (join our Slack here).

Pipeline contribution conventions

To make the nf-core/eager code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.

Adding a new step

If you wish to contribute a new step, please use the following coding standards:

1. Define the corresponding input channel into your new process from the expected previous process channel
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new flags/options to nextflow.config with a default (see below).
5. Add any new flags/options to nextflow_schema.json with help text (with nf-core schema build .).
6. Add sanity checks for all relevant parameters.
7. Add any new software to the scrape_software_versions.py script in bin/ and the version command to the scrape_software_versions process in main.nf.
8. Do local tests that the new code works properly and as expected.
9. Add a new test command in .github/workflow/ci.yaml.
10. If applicable add a MultiQC module.
11. Update MultiQC config assets/multiqc_config.yaml so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
12. Optional: Add any descriptions of MultiQC report sections and output files to docs/output.md.

Default values

Parameters should be initialised / defined with default values in nextflow.config under the params scope.

Once there, use nf-core schema build . to add to nextflow_schema.json.

Default processes resource requirements

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in conf/base.config. These should generally be specified generic with withLabel: selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the nf-core pipeline template, which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

⚠️ Note that in nf-core/eager we currently have our own custom process labels, so please check base.config!

The process resources can be passed on to the tool dynamically within the process with the ${task.cpu} and ${task.memory} variables in the script: block.

Naming schemes

Please use the following naming schemes, to make it easy to understand what is going where.

• initial process channel: ch_output_from_<process>
• intermediate and terminal channels: ch_<previousprocess>_for_<nextprocess>
• skipped process output: ch_<previousstage>_for_<skipprocess>(this goes out of the bypass statement described above)

Nextflow version bumping

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: nf-core bump-version --nextflow . [min-nf-version]

Software version reporting

If you add a new tool to the pipeline, please ensure you add the information of the tool to the get_software_version process.

Add to the script block of the process, something like the following:

<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true

or

<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true

You then need to edit the script bin/scrape_software_versions.py to:

1. Add a Python regex for your tool's --version output (as in stored in the v_<YOUR_TOOL>.txt file), to ensure the version is reported as a v and the version number e.g. v2.1.1
2. Add a HTML entry to the OrderedDict for formatting in MultiQC.

Images and figures

For overview images and other documents we follow the nf-core style guidelines and examples.

For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here here.

Process Concept

We are providing a highly configurable pipeline, with many options to turn on and off different processes in different combinations. This can make a very complex graph structure that can cause a large amount of duplicated channels coming out of every process to account for each possible combination.

The EAGER pipeline can currently be broken down into the following 'stages', where a stage is a collection of non-terminal mutually exclusive processes, which is the output of which is used for another file reporting module (but not reporting!) .

• Input
• Convert BAM
• PolyG Clipping
• AdapterRemoval
• Mapping (either bwa, bwamem, or circularmapper)
• BAM Filtering
• Deduplication (either dedup or markduplicates)
• BAM Trimming
• PMDtools
• Genotyping

Every step can potentially be skipped, therefore the output of a previous stage must be able to be passed to the next stage, if the given stage is not run.

To somewhat simplify this logic, we have implemented the following structure.

The concept is as follows:

• Every 'stage' of the pipeline (i.e. collection of mutually exclusive processes) must always have a if else statement following it.
• This if else 'bypass' statement collects and standardises all possible input files into single channel(s) for the next stage.
• Importantly - within the bypass statement, a channel from the previous stage's bypass mixes into these output channels. This additional channel is named ch_previousstage_for_skipcurrentstage. This contains the output from the previous stage, i.e. not the modified version from the current stage.
• The bypass statement works as follows:
  • If the current stage is turned on: will mix the previous stage and current stage output and filter for file suffixes unique to the current stage output
  • If the current stage is turned off or skipped: will mix the previous stage and current stage output. However as there there is no files in the output channel from the current stage, no filtering is required and the files in the 'ch_XXX_for_skipXXX' stage will be used.

This ensures the same channel inputs to the next stage is 'homogeneous' - i.e. all comes from the same source (the bypass statement)

An example schematic can be given as follows

 // PREVIOUS STAGE OUTPUT
if (params.run_bam_filtering) {
    ch_input_for_skipconvertbam.mix(ch_output_ch_convertbam)
        .filter{ it =~/.*converted.fq/}
        .into { ch_convertbam_for_fastp; ch_convertbam_for_skipfastp }
} else {
    ch_input_for_skipconvertbam
        .into { ch_convertbam_for_fastp; ch_convertbam_for_skipfastp }
}

// SKIPPABLE CURRENT STAGE PROCESS
process fastp {
    publishDir "${params.outdir}/fastp", mode: 'copy'

    when:
    params.run_fastp

    input:
    file fq from ch_convertbam_for_fastp

    output:
    file "*pG.fq" into ch_output_from_fastp

    script:
    """
    echo "I have been fastp'd" > ${fq}  
    mv ${fq} ${fq}.pG.fq
    """
}

// NEXT STAGE INPUT PREPARATION
if (params.run_fastp) {
    ch_convertbam_for_skipfastp.mix(ch_output_from_fastp)
        .filter { it =~/.*pG.fq/ }
        .into { ch_fastp_for_adapterremoval; ch_fastp_for_skipadapterremoval }
} else {
    ch_convertbam_for_skipfastp
        .into { ch_fastp_for_adapterremoval; ch_fastp_for_skipadapterremoval }
}