[Failed Analysis]: Wrong manta install_path - Githubissues

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

https://balsamic.readthedocs.io/

MIT License

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[Failed Analysis]: Wrong manta install_path #776

Closed ashwini06 closed 3 years ago

ashwini06 commented 3 years ago

While running the case equalbug (TN), the workflow fails with manta rule. Check the screenshot for error

Screenshot 2021-09-28 at 11 10 10

Solution:

The path here https://github.com/Clinical-Genomics/BALSAMIC/blob/dd4e99ebe67d541aa3d889037447ffc4f5ee0de3/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule#L32 needs to corrected with proper one.

References and other implementations Also T-only manta https://github.com/Clinical-Genomics/BALSAMIC/blob/dd4e99ebe67d541aa3d889037447ffc4f5ee0de3/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule#L28

hassanfa commented 3 years ago

The new path should be: /opt/conda/share/manta-1.6.0-1/libexec/convertInversion.py

ashwini06 commented 3 years ago

Fixed in #781