From 0f427397b5a52b2696ca213117eecb180f5f3f39 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 5 May 2022 18:38:03 +0200
Subject: [PATCH] [LINT] fix
---
nextflow_schema.json | 2 +-
subworkflows/local/input_check.nf | 2 ++
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9aa8807..6e603ea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -58,7 +58,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
- "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+ "pattern": "^\\S+\\.fn?s?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index c8582b0..999d1e3 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -13,6 +13,7 @@ workflow INPUT_CHECK {
if (params.split_fastq){
SAMPLESHEET_CHECK ( samplesheet )
+ .csv
.splitCsv ( header:true, sep:',' )
.map { create_fastq_channels(it) }
.splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
@@ -25,6 +26,7 @@ workflow INPUT_CHECK {
}else{
SAMPLESHEET_CHECK ( samplesheet )
+ .csv
.splitCsv ( header:true, sep:',' )
.map { create_fastq_channels(it) }
.map { it -> [it[0], [it[1], it[2]]]}
--
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