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Gregor Sturm 2020-07-15 13:29:21 +02:00
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@ -54,20 +54,23 @@ nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
## Adding a new module file ## Adding a new module file
If you decide to upload your module file to `nf-core/modules` then this will ensure that it will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within the Nextflow community! See [`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software) for examples. If you decide to upload your module file to `nf-core/modules` then this will
ensure that it will be automatically downloaded, and available at run-time to
all nf-core pipelines, and to everyone within the Nextflow community! See
[`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software)
for examples.
The definition and standards for module files are still under discussion amongst the community. **The definition and standards for module files are still under discussion
amongst the community. Currently the following points have been agreed on:**
Currently the following points have been agreed on:
The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119). The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119).
### Defining inputs, outputs and parameters ### Defining inputs, outputs and parameters
- Module files SHOULD only define inputs and outputs as parameters. Additionally, - A module file SHOULD only define inputs and outputs as parameters. Additionally,
- it MUST define threads or resources where required for a particular process using `task.cpus` - it MUST define threads or resources where required for a particular process using `task.cpus`
- It MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_options` parameter. - it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.
- All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13) - All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13).
- Process names MUST be all uppercase - Process names MUST be all uppercase.
- Each process MUST emit a file `<TOOL>.version.txt` containing a single line with the software's version in the format `v<VERSION_NUMBER>`. - Each process MUST emit a file `<TOOL>.version.txt` containing a single line with the software's version in the format `v<VERSION_NUMBER>`.
- All outputs MUST be named using `emit`. - All outputs MUST be named using `emit`.
@ -75,10 +78,12 @@ The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as descri
- Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM. - Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM.
### Publishing results ### Publishing results
- The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
- The `publishDirMode` MUST be configurable via `params.publish_dir_mode` - The `publishDirMode` MUST be configurable via `params.publish_dir_mode`
- The module MUST accept a parameter `params.publish_results` accepting at least - The module MUST accept a parameter `params.publish_results` accepting at least
- `"none"`, to publish no files at all, and - `"none"`, to publish no files at all, and
- `"default"`, to publish a sensible selection of files. - `"default"`, to publish a sensible selection of files.
It MAY accept further options. It MAY accept further options.
- To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them. - To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them.