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feat added tests for stubs
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Lucpen
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10 changed files with 101 additions and 0 deletions
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@ -14,3 +14,14 @@ workflow test_gatk4_mergebamalignment {
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GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
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}
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workflow test_gatk4_mergebamalignment_stubs {
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input = [ [ id:'test' ], // meta map
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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 = 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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@ -7,3 +7,12 @@
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- path: output/gatk4/test.bam
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md5sum: e6f1b343700b7ccb94e81ae127433988
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- path: output/gatk4/versions.yml
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- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
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command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/mergebamalignment
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files:
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- path: output/gatk4/test.bam
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- path: output/gatk4/versions.yml
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@ -118,3 +118,21 @@ workflow test_gatk4_mutect2_mitochondria {
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GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
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}
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workflow test_gatk4_mutect2_tumor_single_stubs {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], 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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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 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
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}
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@ -69,3 +69,14 @@
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md5sum: fc6ea14ca2da346babe78161beea28c9
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single_stubs
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/mutect2
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.stats
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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@ -11,3 +11,11 @@ workflow test_gatk4_revertsam {
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GATK4_REVERTSAM ( input )
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}
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workflow test_gatk4_revertsam_stubs {
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input = [ [ id:'test' ], // meta map
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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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}
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@ -7,3 +7,12 @@
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- path: output/gatk4/test.reverted.bam
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md5sum: f783a88deb45c3a2c20ca12cbe1c5652
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- path: output/gatk4/versions.yml
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- name: gatk4 revertsam test_gatk4_revertsam_stubs
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command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/revertsam
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files:
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- path: output/gatk4/test.reverted.bam
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- path: output/gatk4/versions.yml
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@ -19,3 +19,11 @@ workflow test_gatk4_samtofastq_paired_end {
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GATK4_SAMTOFASTQ ( input )
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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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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
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]
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GATK4_SAMTOFASTQ ( input )
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}
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@ -19,3 +19,13 @@
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- path: output/gatk4/test_2.fastq.gz
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md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
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- path: output/gatk4/versions.yml
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- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
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command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/samtofastq
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files:
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- path: output/gatk4/test_1.fastq.gz
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- path: output/gatk4/test_2.fastq.gz
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- path: output/gatk4/versions.yml
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@ -22,3 +22,12 @@ workflow test_samtools_view_cram {
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SAMTOOLS_VIEW ( input, fasta )
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}
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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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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
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[]
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]
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SAMTOOLS_VIEW ( input, [] )
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}
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@ -14,3 +14,11 @@
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- samtools
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files:
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- path: output/samtools/test.cram
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- name: samtools view test_samtools_view_stubs
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command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
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tags:
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- samtools/view
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- samtools
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files:
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- path: output/samtools/test.bam
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