From dbbbac3011e1bff6d893c3f6596daeb755156c6d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 18:52:31 +0200
Subject: [PATCH] CONTRIBUTING.md: add info on channel creation
---
CONTRIBUTING.md | 17 +++++++++++++++++
src/nf_modules/bowtie2/main.nf | 2 +-
2 files changed, 18 insertions(+), 1 deletion(-)
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index e40f4a60..1f341df9 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -130,6 +130,23 @@ If you want to use information within the `file_id` to name outputs in your `scr
```
and use the `file_prefix` variable.
+This also means that channel emitting `path` item should be transformed with at least the following map function:
+
+```
+.map { it -> [it.simpleName, it]}
+````
+
+for example:
+
+```
+channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .map { it -> [it.simpleName, it]}
+ .set { fasta_files }
+```
+
+
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
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 1dc0780d..efd0ceb3 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -46,7 +46,7 @@ process mapping_fastq {
tuple val(file_id), path(reads)
output:
- tuple val(file_id), path("*.bam"), emit: bam
+ tuple val(), path("*.bam"), emit: bam
path "*_report.txt", emit: report
script:
--
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