From 020a69e456f1dd6f9ffab6a9315113cc0440074b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 11:12:22 +0200
Subject: [PATCH] CONTRIBUTING.md: end of the nf_modules section
---
CONTRIBUTING.md | 57 ++++++++++++++++++++++++++++++++++++++++++++++---
1 file changed, 54 insertions(+), 3 deletions(-)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 476e47f2..e40f4a60 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -118,17 +118,68 @@ process fastp {
Here `file_id` can be anything from a simple identifier to a list of several variables.
So you have to keep that in mind if you want to use it to define output file names (you can test for that with `file_id instanceof List`).
+If you want to use information within the `file_id` to name outputs in your `script` section, you can use the following snipet:
+
+```
+ script:
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
+ }
+```
+and use the `file_prefix` variable.
+
The rational behind taking a `file_id` and emitting the same `file_id` is to facilitate complex channel operations in pipelines without having to rewrite the `process` blocks.
### dealing with paired-end and single-end data
-Fastq files opened with `channel.fromFilePairs( params.fastq )`
+Fastq files opened with `channel.fromFilePairs( params.fastq )` create item of the following shape:
+```
+[file_id, [read_1_file, read_2_file]]
+```
+To make this call more generic, we can use the `size: -1` option, and accept arbitrary number of associated fastq file:
-### Handling single and paired end data
+```
+channel.fromFilePairs( params.fastq, size: -1 )
+```
+
+will thus give `[file_id, [read_1_file, read_2_file]]` for paired-end data and `[file_id, [read_1_file]]` for single-end data
-For process that have to deal with single
+```
+...
+ script:
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
+ }
+ if (reads.size() == 2)
+ """
+ fastp --thread ${task.cpus} \
+ ${params.fastp} \
+ --in1 ${reads[0]} \
+ --in2 ${reads[1]} \
+ --out1 ${file_prefix}_R1_trim.fastq.gz \
+ --out2 ${file_prefix}_R2_trim.fastq.gz \
+ --html ${file_prefix}.html \
+ --json ${file_prefix}_fastp.json \
+ --report_title ${file_prefix}
+ """
+ else if (reads.size() == 1)
+ """
+ fastp --thread ${task.cpus} \
+ ${params.fastp} \
+ --in1 ${reads[0]} \
+ --out1 ${file_prefix}_trim.fastq.gz \
+ --html ${file_prefix}.html \
+ --json ${file_prefix}_fastp.json \
+ --report_title ${file_prefix}
+ """
+...
+```
## `src/.docker_modules` guide lines
--
GitLab