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nf-core_modules/tests/modules/gatk4/mutect2/test.yml

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Mutect2 (#682) * mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 15:16:23 +00:00
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.f1r2.tar.gz
- path: output/gatk4/test.vcf.gz
Update for mutect2: add output channel for stats file (#716) * added output channel for stats file, updated meta yml with description and test yml with check for stats file * Update modules/gatk4/mutect2/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 08:56:56 +00:00
- path: output/gatk4/test.vcf.gz.stats
Mutect2 add mitochondria mode and update tests (#967) * 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>
2021-10-29 10:27:56 +00:00
md5sum: 887d54e393510f1d0aa2c33bc6155161
Mutect2 (#682) * mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 15:16:23 +00:00
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.vcf.gz
Update for mutect2: add output channel for stats file (#716) * added output channel for stats file, updated meta yml with description and test yml with check for stats file * Update modules/gatk4/mutect2/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 08:56:56 +00:00
- path: output/gatk4/test.vcf.gz.stats
Mutect2 add mitochondria mode and update tests (#967) * 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>
2021-10-29 10:27:56 +00:00
md5sum: 106c5828b02b906c97922618b6072169
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats
md5sum: 106c5828b02b906c97922618b6072169
Mutect2 (#682) * mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 15:16:23 +00:00
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.vcf.gz
Update for mutect2: add output channel for stats file (#716) * added output channel for stats file, updated meta yml with description and test yml with check for stats file * Update modules/gatk4/mutect2/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 08:56:56 +00:00
- path: output/gatk4/test.vcf.gz.stats
md5sum: 4f77301a125913170b8e9e7828b4ca3f
Mutect2 (#682) * mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 15:16:23 +00:00
- path: output/gatk4/test.vcf.gz.tbi
Mutect2 add mitochondria mode and update tests (#967) * 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>
2021-10-29 10:27:56 +00:00
- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats
md5sum: fc6ea14ca2da346babe78161beea28c9
- path: output/gatk4/test.vcf.gz.tbi
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