Verified Commit b927e7f7 authored by Laurent Modolo's avatar Laurent Modolo
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CONTRIBUTING.md: add complex processes step

parent 1fed060f
......@@ -203,6 +203,40 @@ You can the use tests on `read.size()` to define conditional `script` block:
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### Complex processes
Sometime you want to do write complexe processes, for example for `fastp` we want to have predefine `fastp` process for different protocols, order of adapter trimming and reads clipping.
We can then use the fact that `process` or named `workflow` can be interchangeably imported with th [DSL2](https://www.nextflow.io/docs/latest/dsl2.html#workflow-composition).
With the following example, the user can simply include the `fastp` step without knowing that it's a named `workflow`instead of a `process`.
By specifying the `params.fastp_protocol`, the `fastp` step will transparently switch betwen the different `fastp` `process`es.
Here `fastp_default` or `fastp_accel_1splus`, and other protocols can be added later, pipeline will be able to handle these new protocols by simply updating from the `upstream` repository without changing their codes.
```
params.fastp_protocol = ""
workflow fastp {
take:
fastq
main:
switch(params.fastp_protocol) {
case "accel_1splus":
fastp_accel_1splus(fastq)
fastp_accel_1splus.out.fastq.set{res_fastq}
fastp_accel_1splus.out.report.set{res_report}
break;
default:
fastp_default(fastq)
fastp_default.out.fastq.set{res_fastq}
fastp_default.out.report.set{res_report}
break;
}
emit:
fastq = res_fastq
report = res_report
}
```
## `src/.docker_modules` guide lines
We are going to take the [`fastp`, `.docker_modules`](./src/.docker_module/fastp/0.20.1/) as an example.
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