Merge @swvanderlaan fork to @bglnelissen #29
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This was
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Aug 31, 2021
…s to slideQuantify
…ended echo for cellprofiler run
* Upgrade pipelines & upgrade_study for stains: CD68, EVG, and SR * Upgrade pipelines & upgrade_study for stains: CD34 (DAB & LRP), FIBRIN, and SMA * Updated all pipelines and methods documentation (CD34, CD68, CD66b, EVG, FIBRIN, GLYCC, HE, SMA, SR) --------- Co-authored-by: Tim Peters <[email protected]>
…ne functions, and easier to read.
…or prioritization. Added logic to move and prioritize files.
… Added a requirement of --log.
… extracted from filenames, and padded the number after the dash to 5 digits.
…mbers were not handled properly. Added --stydytype.
…rectly added to the new filename.
…rectly displayed.
…format in a single argument (e.g., "filename.csv csv").
…a conda if it is not found.
…PSS to avoid datetime errors and added installation of pyreadstat.
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We should merge the two forks. There have been a lot of updates, specifically relating to
dmtxandbrew, but also with respect to NDPI-images,python,CellProfiler, and the new HPC submission system (SLURM).