Changes to ParallelEovlCCM.R script.

[Morganthib]

Hello,

I have been running ParallelEvolCCM across several datasets - thanks for making this tool! To make it easier to run across multiple datasets at once, my supervisor @gavinmdouglas and I made a few minor changes:

• Added an option to specify an output directory
• Removed any old chunk files in output directory at start of run. Also renamed temporary chunk files to have the outfile prefix, just in case multiple outputs written to same folder at the same time.
• Added the .gz suffix to the gzipped output table (as this was missing if input was not gzipped)
• Renamed the X2 and pvals outputs from .X2 / .pvals to _X2.tsv / _pvals.tsv, to avoid ambiguity regarding format
• Updated the output globs and stub in modules/local/evolccm.nf to match the new names.

This is the test command we used to run the tool:
Rscript ../arete/bin/ParallelEvolCCM.R --intree tree_subsample.nwk --intable Peccm_format.tsv --outdir peccm_test --cores 1

I have attached the test files used to test the updated script, along with their outputs.
Would you like me to send these changes to your evolCCM repo?

Thank you,

Morgan Thibodeau
Peccm_test_datasets.zip