From 8792d102ee9377ab6886033e3b821dc70df8e5ab Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 12 May 2022 17:37:06 +0200 Subject: [PATCH] fix test input --- tests/modules/gatk4/genotypegvcfs/main.nf | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/tests/modules/gatk4/genotypegvcfs/main.nf b/tests/modules/gatk4/genotypegvcfs/main.nf index 4caba697..cd7d3a03 100644 --- a/tests/modules/gatk4/genotypegvcfs/main.nf +++ b/tests/modules/gatk4/genotypegvcfs/main.nf @@ -82,7 +82,8 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true), + [] ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) @@ -108,6 +109,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input { gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb.add([]) gendb.add([]) + gendb.add([]) input = Channel.of([ id:'test' ]).combine(gendb) @@ -130,6 +132,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp { gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb.add([]) gendb.add([]) + gendb.add([]) input = Channel.of([ id:'test' ]).combine(gendb) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi) @@ -148,6 +151,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals { gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb.add([]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) + gendb.add([]) + input = Channel.of([ id:'test' ]).combine(gendb) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] ) @@ -169,6 +174,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals { gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb.add([]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) + gendb.add([]) + input = Channel.of([ id:'test' ]).combine(gendb) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )