From 192fef094b57278549a662219e3e6783f0bc0b88 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 18 May 2021 10:06:23 +0200
Subject: [PATCH] bowtie2: change file_id handling
---
CONTRIBUTING.md | 15 +++++++++++----
src/nf_modules/bowtie2/main.nf | 14 ++++++++++----
2 files changed, 21 insertions(+), 8 deletions(-)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d3cb5d5e..0f03c1e8 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -125,15 +125,22 @@ process fastp {
Here `file_id` can be anything from a simple identifier to a list of several variables.
In which case the first item of the List should be usable as a file prefix.
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`).
+In some case, the `file_id` may be a Map to have a cleaner access to the `file_id` content by explicit keywords.
If you want to use information within the `file_id` to name outputs in your `script` section, you can use the following snipet:
```Groovy
script:
- if (file_id instanceof List){
- file_prefix = file_id[0]
- } else {
- file_prefix = file_id
+ switch(file_id) {
+ case {it instanceof List}:
+ file_prefix = file_id[0]
+ break
+ case {it instanceof Map}:
+ file_prefix = file_id.values()[0]
+ break
+ default:
+ file_id
+ break
}
```
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 2b0cf963..20f66eb1 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -56,10 +56,16 @@ process mapping_fastq {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
- if (file_id instanceof List){
- file_prefix = file_id[0]
- } else {
- file_prefix = file_id
+ switch(file_id) {
+ case {it instanceof List}:
+ file_prefix = file_id[0]
+ break
+ case {it instanceof Map}:
+ file_prefix = file_id.values()[0]
+ break
+ default:
+ file_id
+ break
}
if (reads.size() == 2)
--
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