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Commit 97d21fae authored by Hanna  JULIENNE's avatar Hanna JULIENNE
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removed glob pattern in preambule

parent c08fac16
Branches jacques
Tags v12.6.0
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...@@ -51,8 +51,8 @@ Region_channel = Channel.fromPath(params.region) ...@@ -51,8 +51,8 @@ Region_channel = Channel.fromPath(params.region)
Region_channel2 = Channel.fromPath(params.region) Region_channel2 = Channel.fromPath(params.region)
chr_channel = Channel.from(1..22) chr_channel = Channel.from(1..22)
ref_chr_channel=Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim") ref_chr_path=params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim"
ld_channel=Channel.fromPath(params.ld_folder)
extract_sample_size_script_channel = Channel.fromPath("${projectDir}/bin/extract_sample_size.py") extract_sample_size_script_channel = Channel.fromPath("${projectDir}/bin/extract_sample_size.py")
generate_trait_pairs_channel = Channel.fromPath("${projectDir}/bin/generate_trait_pairs.py") generate_trait_pairs_channel = Channel.fromPath("${projectDir}/bin/generate_trait_pairs.py")
...@@ -108,8 +108,8 @@ process Impute_GWAS { ...@@ -108,8 +108,8 @@ process Impute_GWAS {
publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy' publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
input: input:
path gwas_files from cleaned_gwas_chr_channel path gwas_files from cleaned_gwas_chr_channel
path ref_file from ref_chr_channel.collect() path ref_file from Channel.fromPath(ref_chr_path).collect()
path ld_file from ld_channel.collect() path ld_file from Channel.fromPath(param.ld_folder).collect()
output: output:
path "imputed_GWAS/*.txt" into imputed_gwas_channel path "imputed_GWAS/*.txt" into imputed_gwas_channel
path "imputed_GWAS/*.txt" into imputed_gwas_channel2 path "imputed_GWAS/*.txt" into imputed_gwas_channel2
......
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