mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
71945a5b5f
* new mitochondria mode added, tests updated to allow for temp fix for test data * add cram test * bam/bam_idx renamed to input and input_index Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
55 lines
2 KiB
YAML
55 lines
2 KiB
YAML
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
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command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c tests/config/nextflow.config
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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.f1r2.tar.gz
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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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md5sum: 887d54e393510f1d0aa2c33bc6155161
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
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command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c tests/config/nextflow.config
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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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md5sum: 106c5828b02b906c97922618b6072169
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
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command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c tests/config/nextflow.config
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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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md5sum: 106c5828b02b906c97922618b6072169
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
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command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c tests/config/nextflow.config
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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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md5sum: 4f77301a125913170b8e9e7828b4ca3f
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- path: output/gatk4/test.vcf.gz.tbi
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- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
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command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c tests/config/nextflow.config
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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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md5sum: fc6ea14ca2da346babe78161beea28c9
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- path: output/gatk4/test.vcf.gz.tbi
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