@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/cutandrun, the standard workflow is
* If there isn't one already, please create one so that others know you're working on this
2.[Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/cutandrun repository](https://github.com/nf-core/cutandrun) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/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](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -69,12 +69,12 @@ If you wish to contribute a new step, please use the following coding standards:
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 .`).
5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
7. Add sanity checks for all relevant parameters.
8. 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`.
9. Do local tests that the new code works properly and as expected.
10. Add a new test command in `.github/workflow/ci.yaml`.
10. Add a new test command in `.github/workflow/ci.yml`.
11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
12. 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.
13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
@@ -83,11 +83,11 @@ If you wish to contribute a new step, please use the following coding standards:
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`.
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](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), 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.
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](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), 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.
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.
