Changelog

[1.12.0] - 2022-09-02

Changed

Change the run_clustal_omega script to perform alignment at amino acid level. This change is motivated by the fact that sometimes the nucleic acid alignment produces sequences containing stop codons which are not valid for subsequent anaylsis steps.

[1.11.1] - 2022-09-01

Fixed

Make run_FUBAR script fail when the errors.log file is produced by FUBAR. This way the pipeline task fails and tasks depending on it are aborted by Compi.

[1.11.0] - 2021-05-10

Changed

Improve the run_FUBAR script to run every analysis from a different working directory.

Fixed

Fix codeML stopping when analyzing files with long names.

Added

clean_working_dir script to clean the working directory.

[1.10.0] - 2021-04-28

Changed

Update Compi version to 1.4.0.

[1.9.0] - 2020-12-21

Changed

Add files that fail to be analized in codeML to the files_requiring_attention list.

[1.8.0] - 2020-12-10

Changed

Remove the check-file-names task.

[1.7.1] - 2020-12-07

Fixed

Fix a bug when running codeML with long file names.

[1.7.0] - 2020-11-08

Changed

Update Compi version to 1.3.7.

[1.6.0] - 2020-11-07

Changed

Update Compi version to 1.3.6.

[1.5.0] - 2020-11-04

Added

Check if the input files have the minimum number of sequences.

Fixed

Fix the prepare trees for codeML step to avoid issues with concurrent seds on the same directory. This is because it was noticed that using a high number of concurrent Compi tasks (e.g. 50) caused some trees to not be created without any obvious reason. However, they were created when running only the foreach tasks for only those files.
Fix a bug when checking FUBAR errors to remove files from the codeML run list.

[1.4.0] - 2020-10-27

Changed

Update Compi version to 1.3.5.

[1.3.0] - 2020-10-26

Added

Now the rename headers script produces also renaming files containing the mappings from the original sequence headers. This allows users of the pipeline to know exactly the names of the sequences in intermediate renamed files that can be produced by the pipeline.

Changed

Update Compi version to 1.3.4.

[1.2.0] - 2020-09-09

Changed

Update Compi version to 1.3.0.
Use binded foreachs.

[1.1.1] - 2020-01-09

Changed

Update Compi version to 1.2.0.

[1.1.0] - 2019-12-19

Changed

Update paml version to 4.9j.

[1.0.0] - 2019-08-07

Added

First public release of the pipeline.