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

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New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
tags:
- gatk4
- gatk4/indexfeaturefile
files:
- path: output/gatk4/genome.bed.idx
Improve syntax/logic coherence in all gatk4 plugins (#1459) * feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 15:15:39 +00:00
- path: output/gatk4/versions.yml
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
tags:
- gatk4
- gatk4/indexfeaturefile
files:
- path: output/gatk4/genome.bed.gz.tbi
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
md5sum: 4bc51e2351a6e83f20e13be75861f941
- path: output/gatk4/versions.yml
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
tags:
- gatk4
- gatk4/indexfeaturefile
files:
- path: output/gatk4/test.genome.vcf.idx
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
- path: output/gatk4/versions.yml
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
tags:
- gatk4
- gatk4/indexfeaturefile
files:
- path: output/gatk4/test.genome.vcf.gz.tbi
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
md5sum: fedd68eaddf8d31257853d9da8325bd3
- path: output/gatk4/versions.yml
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