Beta version 2.3

D4_Portable is currently configured to be the closest to the original pipeline D4_Clinical ("bash" version).

It has:

• deWave disabled (it can be enabled in the config.yml file);
• QDNAseq's segmentBins was it parameters in default (alpha = 1e-10, SD = 1);
  - segmentBins alpha and SD values are adjustable in the config.yml file;
• New - new calibration profiles avaliable for ionTurrent reads;
• New - able to run in Docker like container imagem, with Podman.

Overall, the D4_Portable in previous release was having some problems, such as over-segmentation, in some copy number profiles (illumina). Was found out that deWave may cause the over-segmentation problem, even by adjusting the segmentBins parameters alpha and SD (was possible to "fix" some of the over-segmentation) was decided to keep the pipeline setting closest to D4_Clinical. Therefore, disabling deWaving, until it's calibration update with the new normals; and segmentBins as default.

| Also, was considered to not exceed over the ~300 segments (over-segmentation). |

Obs: Some tests were preformed with profiles from Thermo Fisher Ion Torrent, these had a much lower reads and lower tumor percentage. Was found out that, profile with a low tumor percentage with less than 800 reads are completely unanalysable. If it has between 1M - 800 reads , it could be analysable but it depends in its tumor percentage.

| Maybe, consider ~30, or ~20, segments as the acceptable minimum? |

Still TO DO:

• Test the remaining cell-lines (profiles), Ion Torrent;
• Update/calibrate deWave with the new normals (illumnia and Ion Torrent); (still need the ones for illumina)
• Replace clonality script with the newest version;
• Adjust conda environment file, if needed; (still needs to be optimized)
• Finish container (dockerfile), and upload to docker hub. (still needs to be optimized)