Code

Clean up code#9

Code

Merged

nbtm-sh merged 22 commits intounsw-devAustralian-Structural-Biology-Computing/proteinfold:unsw-devfrom clean-up-codeAustralian-Structural-Biology-Computing/proteinfold:clean-up-codeCopy head branch name to clipboardOct 10, 2024

+165-69

Commits

Commits on Aug 8, 2024

• feat(conf/dbs): Added variables for database names, and file names

  nbtm-sh

  committed
  964f5d0

• feat(conf/dbs): Changed config paths to use database variables instead of hardcoded values

  nbtm-sh

  committed
  2a79fe4

• feat(run_alphafold2): Changed hardcoded paths to use variables and updated variable names

  nbtm-sh

  committed
  c218ad2

• feat(run_alphafold2_msa): Removed hardcoded paths and changed variables

  nbtm-sh

  committed
  edff052

• feat(run_alphafold2_msa): Added code from run_alphafold2.nf so that the script does not attempt to modify the existing database file

  nbtm-sh

  committed
  ea4459a

• fix(conf/dbs): Changed variable names to have _prefix on the end to avoid conflicts with existing link variables

  nbtm-sh

  committed
  83ca302

• fix(conf/dbs): Changed existing variables to use new prefix variables

  nbtm-sh

  committed
  faba0ab

• feat(nextflow.config): Added new param variables and defaults to the config file

  nbtm-sh

  committed
  04cad9d

Commits on Aug 9, 2024

• feat(dbs): Made variables global

  nbtm-sh

  committed
  afeb122

Commits on Aug 16, 2024

• fix(dbs): Changed database directory default

  nbtm-sh

  committed
  3d615b7

• feat(katana): Temporarily removed PBS job scheduling

  nbtm-sh

  committed
  cb29256

• fix(run_alphafold2): Fixed copy command to point to the correct directory

  nbtm-sh

  committed
  5829301

• fix(run_alphafold2): Updated paths to point to the correct uniclust databse

  nbtm-sh

  committed
  485e400

• fix(run_alphafold2): Fixed typo

  nbtm-sh

  committed
  d008f38

• feat(run_alphafold2): Added symlink for params file

  nbtm-sh

  committed
  a0dbd9c

• feat(nextflow): Changed default to use GPU

  nbtm-sh

  committed
  598cc26

• feat(nextflow): Included katana config

  nbtm-sh

  committed
  eba4412

• feat(test): Added options to katana tests

  nbtm-sh

  committed
  4811d3c

• revert(nextflow): Changed default GPU to false

  nbtm-sh

  committed
  9212111

• revert(nextflow): Changed config back to base config

  nbtm-sh

  committed
  0795469

Commits on Sep 5, 2024

• feat(katana): Added katana config

  nbtm-sh

  committed
  5fe8e1d

Commits on Oct 10, 2024

• feat(style): pushing uncommited changes

  nbtm-sh

  committed
  9af55b1