Module for Sentieons gvcftyper

[asp8200]

@maxulysse : Let me know what you think :-)

The new test tests/modules/nf-core/sentieon/genotyper/test.yml is pretty much just a copy of the one for GATK's genotyper.

There are fewer individual tests in tests/modules/nf-core/sentieon/genotyper/test.yml than in the corresponding GATK test-yml,, since Sentieons Genotyper apparently doesn't have the genome reference dict as an option.

I had to adjust the annotation-strings which are being checked for in tests/modules/nf-core/sentieon/genotyper/test.yml. Here I've tried to document how I had to change the annotation-strings.

Test:

- name: sentieon genotyper test_sentieon_genotyper_vcf_input
  command: nextflow run ./tests/modules/nf-core/sentieon/genotyper -entry test_sentieon_genotyper_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/genotyper/nextflow.config

• ExcessHet changed from 0.0000 to 3.0103.
• QD changed from fra 0.95 to 0.84.
• MQ (60.00) removed.
• ReadPosRankSum changed from 1.09 to 1.092. (Just added a digit. That is not important.)

Test:

- name: sentieon genotyper test_sentieon_genotyper_gz_input_dbsnp
  command: nextflow run ./tests/modules/nf-core/sentieon/genotyper -entry test_sentieon_genotyper_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/genotyper/nextflow.config

Same changes (me thinks).

Test:

- name: sentieon genotyper test_sentieon_genotyper_gz_input_intervals
  command: nextflow run ./tests/modules/nf-core/sentieon/genotyper -entry test_sentieon_genotyper_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/genotyper/nextflow.config

Same changes.

Test:

- name: sentieon genotyper test_sentieon_genotyper_gz_input_dbsnp_intervals
  command: nextflow run ./tests/modules/nf-core/sentieon/genotyper -entry test_sentieon_genotyper_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/genotyper/nextflow.config

• ExcessHet changed from 0.0000 to 3.0103.
• QD changed from 24.05 to 23.34
• DB removed.

Test:

- name: sentieon genotyper test_sentieon_genotyper_gz_input_dbsnp_intervals
  command: nextflow run ./tests/modules/nf-core/sentieon/genotyper -entry test_sentieon_genotyper_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/genotyper/nextflow.config

• DB added.

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[maxulysse]

tests appear to be failing

[asp8200]

tests appear to be failing

Yeah, I changed the module name and messed around with that a bit. Now the tests should start to pass again :-)

[maxulysse]

ok to merge