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fix datatest for stubs

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This commit is contained in:
Lucpen 2022-05-06 15:34:18 +02:00
parent 0fa36e6777
commit 971a17a3ab
5 changed files with 20 additions and 20 deletions
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8
tests/modules/gatk4/mergebamalignment/main.nf
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@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
workflow test_gatk4_mergebamalignment_stubs { workflow test_gatk4_mergebamalignment_stubs {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
"test_foo.bam", file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
"test_bar.bam" file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
] ]
fasta = "genome.fasta" fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dict = "genome.fasta.dict" dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict ) GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
} }

24
tests/modules/gatk4/mutect2/main.nf
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@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
} }
workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs { workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
[ "foo_paired.bam", [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
"foo_paired2.bam" file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
], ],
[ "foo_paired.bam.bai", [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
"foo_paired2.bam.bai" file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
], ],
[] []
] ]
fasta = "genome.fasta" fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = "genome.fasta.fai" fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dict = "genome.fasta.dict" dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
germline_resource = "genome_gnomAD.r2.1.1.vcf.gz" germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi" germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz" panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi" panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) GATK4_MUTECT2_F1R2 ( 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
"foo_paired_end.bam" file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
GATK4_REVERTSAM ( input ) GATK4_REVERTSAM ( input )

4
tests/modules/gatk4/samtofastq/main.nf
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@ -21,8 +21,8 @@ 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: true ], // meta map
[ "foo_paired_end.bam" ] [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
] ]
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
"foo_paired_end.bam", file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[] []
] ]