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

- name: gatk4 applybqsr test_gatk4_applybqsr_spark
  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
  tags:
    - gatk4
    - gatk4/applybqsrspark
  files:
    - path: output/gatk4/test.bam
      md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
    - path: output/gatk4/versions.yml

- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
  tags:
    - gatk4
    - gatk4/applybqsrspark
  files:
    - path: output/gatk4/test.bam
    - path: output/gatk4/versions.yml

- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
  tags:
    - gatk4
    - gatk4/applybqsrspark
  files:
    - path: output/gatk4/test.cram
      md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
    - path: output/gatk4/versions.yml
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			`- name: gatk4 applybqsr test_gatk4_applybqsr_spark`
			`command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config`
			`tags:`
			`- gatk4`
			`- gatk4/applybqsrspark`
			`files:`
			`- path: output/gatk4/test.bam`
Update md5sums 2022-05-12 14:07:12 +00:00			`md5sum: 1901c819fcba0fdd5e2482e6dc8285ef`
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`

			`- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals`
			`command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config`
			`tags:`
			`- gatk4`
			`- gatk4/applybqsrspark`
			`files:`
			`- path: output/gatk4/test.bam`
			`- path: output/gatk4/versions.yml`

			`- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram`
			`command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config`
			`tags:`
			`- gatk4`
			`- gatk4/applybqsrspark`
			`files:`
			`- path: output/gatk4/test.cram`
Update md5sums 2022-05-12 14:07:12 +00:00			`md5sum: 60f7c822a9f2833e11eb7bfd16e4421f`
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`