Update estimate_tumor_normal_contaminations.py to take inputs from a file instead of command line parameters

mskcc / Conpair

Concordance and contamination estimator for tumor-normal pairs

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Update estimate_tumor_normal_contaminations.py to take inputs from a file instead of command line parameters #7

Closed allanbolipata closed 4 years ago

allanbolipata commented 4 years ago

Currently conpair uses separate flags for tumor and normal pileup files (https://github.com/mskcc/Conpair/blob/master/scripts/estimate_tumor_normal_contaminations.py#L49-L50); this causes the command to get too large for command line and singularity when there are a lot of samples, breaking operation.

Update it so that it takes in an input file containing references to the pileup files instead.

@timosong please clarify any issues here. Alternative suggestions are also welcome.

stevekm commented 4 years ago

this should be resolved in the new dev branch Right now, that implementation is using two files, tumors.txt and normals.txt, with lists of file paths to the input files.