Commits · containerized_2 · Astrocyte / Workflows / BICF / chipseq_analysis

Feb 28, 2025
- updated queues of some intensive processes · 132f40a8
  Thamer Alsulaiman authored 1 week ago
  
  2 tags
  
  132f40a8
Feb 27, 2025
- reversing memory change in map_reads.py · 5add902e
  Thamer Alsulaiman authored 2 weeks ago
  
  test_1.2.16
  
  5add902e
Oct 30, 2024
- Removed debugging code and fixed memory_per_thread assignment · 45521260
  Thamer Alsulaiman authored 4 months ago
  
  test_1.2.15
  
  45521260
Oct 16, 2024
- removed dev files -- files committed by mistake · 3db8ba62
  Thamer Alsulaiman authored 4 months ago
  
  3db8ba62
Sep 04, 2024
- updated executor for all processes · f4474da5
  Thamer Alsulaiman authored 6 months ago
  
  2 tags
  
  f4474da5
Aug 28, 2024
- fixed memory assignment per thread to whole memory scaled to 0.7; updated queues for some processes · 1309b519
  Thamer Alsulaiman authored 6 months ago
  
  test_1.2.12
  
  1309b519
Aug 27, 2024
- all processes run on 128GB or higher machines · 6f728d3f
  Thamer Alsulaiman authored 6 months ago
  
  test_1.2.11
  
  6f728d3f
Aug 22, 2024
- limit number of concurrent processes in trimreads, alignreads, and filterreads... · 212a45f8
  Thamer Alsulaiman authored 6 months ago
```
limit number of concurrent processes in trimreads, alignreads, and filterreads to 4 to help with memory issues
```
  212a45f8
- in convert_reads.py: assigned memory to working thread in damtool sort, similar to map_reads.py · fef9b644
  Thamer Alsulaiman authored 6 months ago
  
  fef9b644
Aug 21, 2024
- quadruple memory used per thread in alignread step in mapreads.py script · 8a65eeba
  Thamer Alsulaiman authored 6 months ago
  
  8a65eeba
- updated main to use back python docker with entrypoint · d7b5e667
  Thamer Alsulaiman authored 6 months ago
  
  d7b5e667
Aug 20, 2024
- Using py36 docker with no-conda env and updating related files. Use nextflow 19 · b755c158
  Thamer Alsulaiman authored 6 months ago
  
  b755c158
Aug 12, 2024
- Dummy commit -- to force updating master · 278fecea
  Thamer Alsulaiman authored 7 months ago
  
  278fecea
Jul 30, 2024
- changed nextflow version to 22.x.y · 3df76e37
  Thamer Alsulaiman authored 7 months ago
  
  3df76e37
- Added argument to call of ifEmpty() · f79d991e
  Thamer Alsulaiman authored 7 months ago
  
  f79d991e
Jul 29, 2024
- Uncommented nextflow_version in astrocyte_pkg.yml · ae771b45
  Thamer Alsulaiman authored 7 months ago
  
  ae771b45
Jul 28, 2024
- Use 256 queue only for trim reads step to avoid samtools call in map_reads.py:wq · 967242be
  Thamer Alsulaiman authored 7 months ago
  
  967242be
Jul 22, 2024
- Add missing port number to container image tags. · 6c0883b3
  Felix Perez authored 7 months ago
  
  6c0883b3
- Rewrite container image references in the workflow config files to use the... · dd5d9a37
  Felix Perez authored 7 months ago
```
Rewrite container image references in the workflow config files to use the official container registry.
```
  dd5d9a37
Jul 19, 2024
- Merge branch 'containerized' into 'containerized' · 447688b0
  Felix Perez authored 7 months ago
```
Added new Docker file for motif search (named meme-5.5.4) installed from...

See merge request !1
```
  447688b0
Jul 17, 2024

Added new Docker file for motif search (named meme-5.5.4) installed from... · 2430d169

Added new Docker file for motif search (named meme-5.5.4) installed from source, with all the necessary changes to use the new container for motif search. Updated the command line arguments for meme-chip to use v5.x syntax.

2430d169

Jul 16, 2024
- Merge branch 'containerized' of... · d6a8d534
  Felix Perez authored 7 months ago
```
Merge branch 'containerized' of git.biohpc.swmed.edu:s219741/chipseq-analysis-containerized into containerized

Conflicts:
	building/docker/motif-search/Dockerfile
```
  d6a8d534
- FP push final changes to repo before moving. · f1b61220
  Felix Perez authored 7 months ago
  
  f1b61220
Jul 10, 2024
- Update base image tag in Dockerfiles. · ae2932f4
  Felix Perez authored 8 months ago
  
  ae2932f4
May 15, 2024
- Push in-development containerized workflow · fbc41119
  Felix Perez authored 9 months ago
  
  fbc41119
Aug 16, 2020
- Merge branch 'dev' into 'master' · 6eb0e21e
  Venkat Malladi authored 4 years ago
```
Release 1.1.3

See merge request BICF/Astrocyte/chipseq_analysis!73
```
  publish_1.1.3
  
  6eb0e21e
- get ready for release. · e4c84105
  Venkat Malladi authored 4 years ago
  
  e4c84105
Aug 07, 2020
- Merge branch 'issue3087-annotation_fix' into 'dev' · 547c341d
  Venkat Malladi authored 4 years ago
```
Issue3087 annotation fix

Closes #87

See merge request BICF/Astrocyte/chipseq_analysis!72
```
  547c341d
Aug 06, 2020
- update peak annotation pytest · c78024de
  Spencer Barnes authored 4 years ago
  
  c78024de
Aug 04, 2020
- add test to ensure symbol column of peak annotation is not empty · 375b9e56
  Spencer Barnes authored 4 years ago
  
  375b9e56
Aug 03, 2020
- fix peak annotation r script · b5c9ff2e
  Spencer Barnes authored 4 years ago
  
  b5c9ff2e
Jul 01, 2020
- Merge branch '84-astrocyte-upgrade' into 'dev' · 27540804
  Jonathan Gesell authored 4 years ago
```
Update astrocyte to 0.3.1

Closes #84

See merge request BICF/Astrocyte/chipseq_analysis!71
```
  27540804
Jun 26, 2020
- Link to general doi. · 36ed0661
  Venkat Malladi authored 4 years ago
  
  36ed0661
- Add in 0.3.1. support for astrocyte. · fabeb27b
  Venkat Malladi authored 4 years ago
  
  fabeb27b
Jun 22, 2020
- Update reference and version. · e6b416e5
  Venkat Malladi authored 4 years ago
  
  publish_1.1.2
  
  e6b416e5
Jun 21, 2020
- Merge branch '84-tracking' into 'dev' · bb5133f0
  Venkat Malladi authored 4 years ago
```
Add in pipelinetracking.

See merge request BICF/Astrocyte/chipseq_analysis!70
```
  bb5133f0
Jun 19, 2020
- Add in pipelinetracking. · a34ccd98
  Venkat Malladi authored 4 years ago
  
  a34ccd98
Apr 23, 2020
- Update to 1.1.1. · ea6b9d45
  Venkat Malladi authored 4 years ago
  
  publish_1.1.1
  
  ea6b9d45
Apr 22, 2020
- Fix change log. · f0ce60df
  Venkat Malladi authored 4 years ago
  
  f0ce60df
- Add in singularity version is multiqc report. · 5626a6ae
  Venkat Malladi authored 4 years ago
  
  5626a6ae