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chores adding dummy files for stubs

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Lucpen 2022-05-02 13:30:18 +02:00
parent de40c1bf54
commit 3a4e415fe2
4 changed files with 12 additions and 12 deletions
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18
tests/modules/gatk4/mutect2/main.nf
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@ -121,18 +121,18 @@ workflow test_gatk4_mutect2_mitochondria {
workflow test_gatk4_mutect2_tumor_single_stubs { workflow test_gatk4_mutect2_tumor_single_stubs {
input = [ [ id:'test'], // meta map input = [ [ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], [ "foo.bam" ],
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], [ "foo.bam.bai" ],
[] []
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fasta = "genome.fasta"
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) fai = "genome.fasta.fai"
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) dict = "genome.fasta.dict"
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
} }

2
tests/modules/gatk4/revertsam/main.nf
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@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
workflow test_gatk4_revertsam_stubs { workflow test_gatk4_revertsam_stubs {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) "foo_paired_end.bam"
] ]
GATK4_REVERTSAM ( input ) GATK4_REVERTSAM ( input )

2
tests/modules/gatk4/samtofastq/main.nf
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@ -22,7 +22,7 @@ workflow test_gatk4_samtofastq_paired_end {
workflow test_gatk4_samtofastq_paired_end_stubs { workflow test_gatk4_samtofastq_paired_end_stubs {
input = [ [ id:'test', single_end: false ], // meta map input = [ [ id:'test', single_end: false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] [ "foo_paired_end.bam" ]
] ]
GATK4_SAMTOFASTQ ( input ) GATK4_SAMTOFASTQ ( input )

2
tests/modules/samtools/view/main.nf
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@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
workflow test_samtools_view_stubs { workflow test_samtools_view_stubs {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), "foo_paired_end.bam",
[] []
] ]