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fix test input

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This commit is contained in:
Rike 2022-05-12 17:37:06 +02:00
parent a694267b4b
commit 8792d102ee
1 changed files with 8 additions and 1 deletions
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9
tests/modules/gatk4/genotypegvcfs/main.nf
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@ -82,7 +82,8 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
input = [ [ id:'test' ], // meta map 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'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], 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) 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 = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([]) gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) 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 = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([]) gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi) 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 = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] ) 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 = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi ) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )