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fix datatest for stubs
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0fa36e6777
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5 changed files with 20 additions and 20 deletions
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@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
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workflow test_gatk4_mergebamalignment_stubs {
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input = [ [ id:'test' ], // meta map
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"test_foo.bam",
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"test_bar.bam"
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
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]
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fasta = "genome.fasta"
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dict = "genome.fasta.dict"
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
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}
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@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
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}
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workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
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input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
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[ "foo_paired.bam",
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"foo_paired2.bam"
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input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
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],
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[ "foo_paired.bam.bai",
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"foo_paired2.bam.bai"
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
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],
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[]
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]
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fasta = "genome.fasta"
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fai = "genome.fasta.fai"
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dict = "genome.fasta.dict"
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germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
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germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
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panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
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panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
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germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
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panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
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panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
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GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
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}
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@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
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workflow test_gatk4_revertsam_stubs {
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input = [ [ id:'test' ], // meta map
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"foo_paired_end.bam"
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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GATK4_REVERTSAM ( input )
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@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
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}
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workflow test_gatk4_samtofastq_paired_end_stubs {
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input = [ [ id:'test', single_end: false ], // meta map
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[ "foo_paired_end.bam" ]
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input = [ [ id:'test', single_end: true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
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]
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GATK4_SAMTOFASTQ ( input )
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@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
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workflow test_samtools_view_stubs {
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input = [ [ id:'test', single_end:false ], // meta map
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"foo_paired_end.bam",
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
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[]
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]
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