fix: nf-test in strelka

[famosab]

PR checklist

Closes #8031

• 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:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[SPPearce]

Generally good, assuming conda works when rerun

[famosab]

@SPPearce Maybe we can remove conda support for now and add it back in if strelka starts supporting python3?

[SPPearce]

@SPPearce Maybe we can remove conda support for now and add it back in if strelka starts supporting python3?

Hmmm, strelka is used in sarek, I don't think that sounds like a good idea.

[famosab]

@maxulysse Any ideas on this?

[maxulysse]

@maxulysse Any ideas on this?

what was the error?

[maxulysse]

OK, I have seen it this is BAD.
Let's try to figure out what is in the container and reproduce as much as we can in the conda env

[famosab]

Seems to be a known issue with conda: Illumina/strelka#199

[famosab]

@matthdsm If you have any idea how to fix this mess please step up haha (I saw that you solved manta in #9084)

[matthdsm]

Let's try to figure out what is in the container and reproduce as much as we can in the conda env

Packages installed in the container on quay.io

_libgcc_mutex-0.1-conda_forge
_openmp_mutex-4.5-1_gnu
ca-certificates-2020.12.5-ha878542_0
certifi-2019.11.28-py27h8c360ce_1
ld_impl_linux-64-2.35.1-hea4e1c9_2
libffi-3.2.1-he1b5a44_1007
libgcc-ng-9.3.0-h2828fa1_18
libgomp-9.3.0-h2828fa1_18
libstdcxx-ng-9.3.0-h6de172a_18
ncurses-6.2-h58526e2_4
openssl-1.1.1j-h7f98852_0
pip-20.1.1-pyh9f0ad1d_0
python-2.7.15-h5a48372_1011_cpython
python_abi-2.7-1_cp27mu
readline-8.0-he28a2e2_2
setuptools-44.0.0-py27_0
sqlite-3.35.2-h74cdb3f_0
strelka-2.9.10-h9ee0642_1
tk-8.6.10-h21135ba_1
wheel-0.36.2-pyhd3deb0d_0
zlib-1.2.11-h516909a_1010