From b927e7f7cfff3760a9c2155a2b2ecd4d51151f80 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 16 Apr 2021 09:36:48 +0200
Subject: [PATCH] CONTRIBUTING.md: add complex processes step
---
CONTRIBUTING.md | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4cf35d9f..eb2c2500 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -203,6 +203,40 @@ You can the use tests on `read.size()` to define conditional `script` block:
...
```
+### 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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