Feature/refactor kinship print to write

[ellendejong]

What has changed?

Refactor of check_kinship.py

• Changed type from NA to unrelated for unrelated samples.
• Added two new columns:
  • thresholds (string): used kinship settings comma separated, first value is minimum value relatedness and second value is maximum.
  • message (string): user friendly message explaining why kinship check failed. If kinship check succeeded, value is an empty string.
• Used pandas to easily add or edit columns.
• Moved comment statements to start of file (previously last lines)
• Added pytest and docstrings
• Docker container migrated to github packages.

How to

If you want to print output to stdout, use:
check_kinship.py {kinship_file} {ped_file}

If you want to write output to a file use:
check_kinship.py {kinship_file} {ped_file} --output_prefix {prefix} --output_path {/path/to/output}

Examples

Checkout test output.
If all observed kinships values match with expectation based on pedigree file.

cat /hpc/diaggen/software/development/DxNextflowWES_edit_msg/work/49/6db38dc750e0b7e91e0412b8454e41/20240909_0096_8_test_ellen.kinship_check.out

Or if a parent-child relation is missing in pedigree,

cat /hpc/diaggen/software/development/DxNextflowWES_edit_msg/work/d1/11daa552e09b89e3c56e31da1f65cf/20240909_0096_8_test_ellen.kinship_check.out

[fdekievit]

Zou je a.u.b. even kunnen kijken of al deze wijzigingen nodig zijn?

Ik zie b.v. wijzigingen in Mosaic hunter en Utils (wat alleen format wijzigingen zijn) die volgens mij neit relevant zijn voor deze ticket.

[fdekievit]

wat doet pip -U ? en bedacht me net, is er ook een pip3 variant?

[ellendejong]

-U staat voor --upgrade
https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-U

Commando's zijn overgenomen van https://python-poetry.org/docs/#installing-manually

[ellendejong]

pip3 gebruikt in nieuwste commit.

[fdekievit]

Ziet er goed uit