REPET V4 PASTEC release (!2) · Merge requests · URGI-Anagen / REPET-snakemake

Closed BARDET ETIENNE requested to merge dev into main 2 months ago

Jan 27, 2025
- Prototyped step 6 parallelization · 6969d553
  BARDET ETIENNE authored 1 month ago
  
  6969d553
Jan 08, 2025
- fixed error in image pull command · ebaf871c
  BARDET ETIENNE authored 2 months ago
  
  ebaf871c
- updated scripts of TEdenovo · e93b71c4
  BARDET ETIENNE authored 2 months ago
  
  e93b71c4
- updated README of TEannot and PASTEC · 95dff024
  BARDET ETIENNE authored 2 months ago
  
  95dff024
- updated the snakefiles · dfeabb0e
  BARDET ETIENNE authored 2 months ago
  
  dfeabb0e
- updated docs · f9aee914
  BARDET ETIENNE authored 2 months ago
  
  f9aee914
- updated run_snakemake and configs · cf76803d
  BARDET ETIENNE authored 2 months ago
  
  cf76803d
- added Snakefile_conda to PASTEC_snakemake · 082f23f1
  BARDET ETIENNE authored 2 months ago
  
  082f23f1
- updated envs · 455547da
  BARDET ETIENNE authored 2 months ago
  
  455547da
- added conda Snakefile and fixed HMM rules · 69a8f4d7
  BARDET ETIENNE authored 2 months ago
  
  69a8f4d7
Jan 07, 2025
- updated doc · 9356b63b
  BARDET ETIENNE authored 2 months ago
  
  9356b63b
Jan 06, 2025
- fixed bad image naming · 08ff05d6
  BARDET ETIENNE authored 2 months ago
  
  08ff05d6
- updated docs · b8031caa
  BARDET ETIENNE authored 2 months ago
  
  b8031caa
- updated docs · 87be97a6
  BARDET ETIENNE authored 2 months ago
  
  87be97a6
- cleanup of devtools · 4fa79983
  BARDET ETIENNE authored 2 months ago
  
  4fa79983
- removed unused directory · 618616a3
  BARDET ETIENNE authored 2 months ago
  
  618616a3
- Removed the ability to build REPET images from this branch. All the related... · 11d755d8
  BARDET ETIENNE authored 2 months ago
  
  Removed the ability to build REPET images from this branch. All the related files have been moved to the dev_image branch
  11d755d8
- added default banks support to TEdenovo · ad1498eb
  BARDET ETIENNE authored 2 months ago
  
  ad1498eb
- corrected typo · fe5c5d66
  BARDET ETIENNE authored 2 months ago
  
  fe5c5d66
- fixed typos in ProfilesBanks unpacking · a55f9952
  BARDET ETIENNE authored 2 months ago
  
  a55f9952
- removed unused files · e249bf2e
  BARDET ETIENNE authored 2 months ago
  
  e249bf2e
- bundled all the profiles banks into a single archive · 98376c1c
  BARDET ETIENNE authored 2 months ago
  
  98376c1c
- added defaults banks to the sif image, added support for default banks in PASTEC_snakemake · 680ab72e
  BARDET ETIENNE authored 2 months ago
  
  680ab72e
Jan 03, 2025
- Cleanup before merge into main · 5c2c8d28
  BARDET ETIENNE authored 2 months ago
  
  5c2c8d28
Dec 19, 2024
- cleanup · 7132c780
  BARDET ETIENNE authored 2 months ago
  
  7132c780
Dec 12, 2024
- corrected a bug whit TR search and update Snakefiles · 158b8533
  BARDET ETIENNE authored 3 months ago
  
  158b8533
Dec 11, 2024
- changed default value of minBase from 1 to 2 · ff27b8c6
  BARDET ETIENNE authored 3 months ago
  
  ff27b8c6
Dec 10, 2024
- parallelized all of step5 on lostech · 95fb99a6
  BARDET ETIENNE authored 3 months ago
  
  95fb99a6
Dec 09, 2024
- swapped the rest of matcher2.32 for matcher2.25 in lostech snakefile · 9ba1c022
  BARDET ETIENNE authored 3 months ago
  
  9ba1c022
Dec 05, 2024
- reshuffled Step5 Matcher to execute on balster batched results, and modified... · 755804e1
  BARDET ETIENNE authored 3 months ago
  
  reshuffled Step5 Matcher to execute on balster batched results, and modified batching of consensus in step 5
  755804e1
Dec 03, 2024
- added rounding step to filterAlign alignement score · 2ce80cb6
  BARDET ETIENNE authored 3 months ago
  
  2ce80cb6
Dec 02, 2024
- Fixed wrong value in minBasesPerSite in rpt_map.py consensus build step · 0caee63c
  BARDET ETIENNE authored 3 months ago
  
  0caee63c
Nov 25, 2024
- added Snakefile legacy for debuging · ae30a1de
  BARDET ETIENNE authored 3 months ago
  
  ae30a1de
- updated TEdenovo snakefile_conda · 9a0bde25
  BARDET ETIENNE authored 3 months ago
  
  9a0bde25
- updated TEannot config · 7520816a
  BARDET ETIENNE authored 3 months ago
  
  7520816a
- reformated TEannot Snakefiles · d126cbc1
  BARDET ETIENNE authored 3 months ago
  
  d126cbc1
- updated docs · 0b522bb9
  BARDET ETIENNE authored 3 months ago
  
  0b522bb9
Nov 22, 2024
- fixed circular import in NTE/LTE calculation · e7b3a9bf
  BARDET ETIENNE authored 3 months ago
  
  e7b3a9bf
Nov 15, 2024
- fixed bad imports · dbcd7499
  BARDET ETIENNE authored 4 months ago
  
  dbcd7499
- fixed PASTEC in alternative snakefile · d6b383f3
  BARDET ETIENNE authored 4 months ago
  
  d6b383f3
- added alternative snakefile whit no HMM parallelization · 2388bee2
  BARDET ETIENNE authored 4 months ago
  
  2388bee2
Nov 14, 2024
- fixed wildcard in HMM rules and reformated rules · cfbe6a43
  BARDET ETIENNE authored 4 months ago
  
  cfbe6a43
Nov 13, 2024
- parallelised HMM more effectively · 53c07ff8
  BARDET ETIENNE authored 4 months ago
  
  53c07ff8
Nov 06, 2024
- fixed blaster parameters for step 5 in TEdenovo · d75482c8
  BARDET ETIENNE authored 4 months ago
  
  d75482c8
Oct 28, 2024
- Updated the README, removed typos and changed install instructions · fbe5fdf0
  BARDET ETIENNE authored 4 months ago
  
  fbe5fdf0
Oct 24, 2024
- updated TEdenovo to put the PASTEC results in the result dir · 6bb2c246
  BARDET ETIENNE authored 4 months ago
  
  6bb2c246
- removed snakemake from PostProcessClassification · 3c89830e
  BARDET ETIENNE authored 4 months ago
  
  3c89830e
- removed sankemake from PostProcessClassification · b3d026e4
  BARDET ETIENNE authored 4 months ago
  
  b3d026e4
Oct 22, 2024
- updated configs · bdcfeec5
  BARDET ETIENNE authored 4 months ago
  
  bdcfeec5
- moved the TEdenovo steps7 and 8 scripts to common.tools · 5ca2118b
  BARDET ETIENNE authored 4 months ago
  
  5ca2118b
- Changed the Steps 7 and 8 default params to give same results as stock REPET v3 · 3e439aaf
  BARDET ETIENNE authored 4 months ago
  
  3e439aaf
Oct 15, 2024
- updated GetNTE50andLTE50 to be used as stand alone script · 32b89800
  BARDET ETIENNE authored 5 months ago
  
  32b89800
Oct 14, 2024
- started to add NTE50/LTE50 calculation to AnnotStats · e3a5a1c1
  BARDET ETIENNE authored 5 months ago
  
  e3a5a1c1
Oct 10, 2024
- changed the wording of some print statement · 13c600e1
  BARDET ETIENNE authored 5 months ago
  
  13c600e1
- updated GetNTE50AndLTE50 help · 1a010825
  BARDET ETIENNE authored 5 months ago
  
  1a010825
Oct 09, 2024
- renovated split_path_per_chr to actually work · 49da019b
  BARDET ETIENNE authored 5 months ago
  
  49da019b
Oct 04, 2024
- updated cmd lines attribute and added a DoClean option on GetNTE50AndLTE50.py · d2abc35c
  BARDET ETIENNE authored 5 months ago
  
  d2abc35c
Oct 03, 2024
- Updated GetNTE50AndLTE50 to remove TE redundancy in input files · 0f27ba38
  BARDET ETIENNE authored 5 months ago
  
  0f27ba38
Oct 02, 2024

Corrected rare bug in longJoinsForTEs that wopuld search values in an empty... · c517882f

BARDET ETIENNE authored 5 months ago

Corrected rare bug in longJoinsForTEs that wopuld search values in an empty DF, and fixed badNTE50 calculation if fallback is triggered

c517882f

Oct 01, 2024
- added fallback option to NTE50 and LTE50 calculation in case TE coverage < 50% · 332810e3
  BARDET ETIENNE authored 5 months ago
  
  332810e3
- added NTE50 and LTE50 calculation to TEannot · d283725f
  BARDET ETIENNE authored 5 months ago
  
  d283725f
Sep 27, 2024
- replaced script in MCL_clustering and fixed MCL_inflate parameters not being passed to launch_MCL · 8685769c
  BARDET ETIENNE authored 5 months ago
  
  8685769c
Sep 23, 2024
- added NTE50 calculation for TEannot · 43fd8c0f
  BARDET ETIENNE authored 5 months ago
  
  43fd8c0f
Sep 16, 2024
- updated NoCatBestHitClassifier's blaster parameters · 07cf107d
  BARDET ETIENNE authored 5 months ago
  
  07cf107d
- corrected launchBlaster defaults parameters · 9fdbaf5d
  BARDET ETIENNE authored 5 months ago
  
  9fdbaf5d
Sep 12, 2024
- Updated LaunchBlaster.py · 1f3d1974
  BARDET ETIENNE authored 6 months ago
  
  1f3d1974
Sep 11, 2024
- updated LaunchBlaster and started integration in the Snakefiles · dc2a86a5
  BARDET ETIENNE authored 6 months ago
  
  dc2a86a5
- reworked the LaunchBlaster to handle ungapped Karlin-Altschul error · 484b6876
  BARDET ETIENNE authored 6 months ago
  
  484b6876
- fixed some issues whit long join procedure · ea82cd8e
  BARDET ETIENNE authored 6 months ago
  
  ea82cd8e
Sep 10, 2024
- fixed long join procedure itermediary files being out of the result dir · 14f28305
  BARDET ETIENNE authored 6 months ago
  
  14f28305
- parallelized run_long_join in TEannot · a1434531
  BARDET ETIENNE authored 6 months ago
  
  a1434531
Sep 09, 2024
- Updated CI Normalization calculation to use floor division · e8801d95
  BARDET ETIENNE authored 6 months ago
  
  e8801d95
Sep 05, 2024
- updatedPASTEC's SNakefiles and scripts, reformated the TODO · 073047e2
  BARDET ETIENNE authored 6 months ago
  
  073047e2
- updated PASTEC · 469dae27
  BARDET ETIENNE authored 6 months ago
  
  469dae27
- updated TEannot scripts and snakefiles · 496712e9
  BARDET ETIENNE authored 6 months ago
  
  496712e9
- TEdenovo update to scripts and Snakefiles · f5482447
  BARDET ETIENNE authored 6 months ago
  
  f5482447
- updated package build instruction · 2d31dc8c
  BARDET ETIENNE authored 6 months ago
  
  2d31dc8c
Sep 02, 2024
- changed the way PASTEC is called · f263db5b
  BARDET ETIENNE authored 6 months ago
  
  f263db5b
Aug 29, 2024
- experimental fix to allow snakefile import · 41a1ed41
  BARDET ETIENNE authored 6 months ago
  
  41a1ed41
Aug 28, 2024
- fixed PolyA agent and set filters to correct defaults values · cd65c135
  BARDET ETIENNE authored 6 months ago
  
  cd65c135
- fixed SSR_agent bug · b6fdd4d2
  BARDET ETIENNE authored 6 months ago
  
  b6fdd4d2
Aug 20, 2024
- fixed a bug that would cause insignificant results to not be discarded · 8a2e3a7e
  BARDET ETIENNE authored 6 months ago
  
  8a2e3a7e
- updated singularity def files · 2e6d95a8
  BARDET ETIENNE authored 6 months ago
  
  2e6d95a8
Jul 09, 2024
- reshuffled the order of call for all agents, updated the TEname and length on the environnements · 491bc525
  BARDET ETIENNE authored 8 months ago
  
  491bc525
Jun 25, 2024
- fixed bad image calls · 8021eeb0
  BARDET ETIENNE authored 8 months ago
  
  8021eeb0
- changed singularity .def files · 47bb88d7
  BARDET ETIENNE authored 8 months ago
  
  47bb88d7
- added Snakefile_conda to PASTEC · 66ecd512
  BARDET ETIENNE authored 8 months ago
  
  66ecd512
- standardized singularity image call across pipelines · 5be920b6
  BARDET ETIENNE authored 8 months ago
  
  5be920b6
Jun 12, 2024
- continued Long_Join_TE parallelisation · c7ebe1ac
  BARDET ETIENNE authored 9 months ago
  
  c7ebe1ac
Jun 11, 2024
- continued parallelisation of long_join step · d4b9b70f
  BARDET ETIENNE authored 9 months ago
  
  d4b9b70f
Jun 07, 2024
- Started parallelisation of PASTEC step 2 and Long_Join_TE · c58781f5
  BARDET ETIENNE authored 9 months ago
  
  c58781f5
May 30, 2024
- temporary fix for TRsearch and added singularity support · 2ca6d9cf
  BARDET ETIENNE authored 9 months ago
  
  2ca6d9cf
May 29, 2024
- updated the images · 7ae4b93d
  BARDET ETIENNE authored 9 months ago
  
  7ae4b93d
May 24, 2024
- added support for conda and singularity · cb1a53e5
  BARDET ETIENNE authored 9 months ago
  
  cb1a53e5
May 23, 2024
- updated the TODO.md · fec5a169
  BARDET ETIENNE authored 9 months ago
  
  fec5a169
- minor bugfixes on the snakefile · 2ba090e8
  BARDET ETIENNE authored 9 months ago
  
  2ba090e8
- added licenses, began reworking SuperAgent.py to use dict, began to add some test to launchers · e131a228
  BARDET ETIENNE authored 9 months ago
  
  e131a228
May 17, 2024
- Added test to the conda recipe · 514cab4b
  BARDET ETIENNE authored 9 months ago
  
  514cab4b
May 16, 2024
- bugfixes for Blastx, rDNA_blast and HMM rules · 3ebb2e26
  BARDET ETIENNE authored 10 months ago
  
  3ebb2e26
May 14, 2024
- Reworked PASTEC's blaster and Hmmer reliant steps to increase performance, updated doc · 71809635
  BARDET ETIENNE authored 10 months ago
  
  71809635

REPET V4 PASTEC release

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