From 97d21fae38235b2a074974d4b7153acd4eb60ba6 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Fri, 3 Feb 2023 16:42:51 +0100
Subject: [PATCH] removed glob pattern in preambule
---
jass_pipeline.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/jass_pipeline.nf b/jass_pipeline.nf
index 3391106..763a62d 100644
--- a/jass_pipeline.nf
+++ b/jass_pipeline.nf
@@ -51,8 +51,8 @@ Region_channel = Channel.fromPath(params.region)
Region_channel2 = Channel.fromPath(params.region)
chr_channel = Channel.from(1..22)
-ref_chr_channel=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim")
-ld_channel=Channel.fromPath(params.ld_folder)
+ref_chr_path=params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim"
+
extract_sample_size_script_channel = Channel.fromPath("${projectDir}/bin/extract_sample_size.py")
generate_trait_pairs_channel = Channel.fromPath("${projectDir}/bin/generate_trait_pairs.py")
@@ -108,8 +108,8 @@ process Impute_GWAS {
publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
input:
path gwas_files from cleaned_gwas_chr_channel
- path ref_file from ref_chr_channel.collect()
- path ld_file from ld_channel.collect()
+ path ref_file from Channel.fromPath(ref_chr_path).collect()
+ path ld_file from Channel.fromPath(param.ld_folder).collect()
output:
path "imputed_GWAS/*.txt" into imputed_gwas_channel
path "imputed_GWAS/*.txt" into imputed_gwas_channel2
--
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