Commits · master · bird_pipeline_registry / SRP-pipeline

17 May, 2022 2 commits
- updating Dockerfile · d2aa53eb
  Jean-Francois GUILLAUME authored May 17, 2022
  
  d2aa53eb
- adding first iteration of Dockerfile · 765058d6
  Jean-Francois GUILLAUME authored May 17, 2022
  
  765058d6
11 May, 2022 1 commit
- defined fontconfig version in conda env. Last dev release does not work. · b3b483fb
  Eric CHARPENTIER authored May 11, 2022
  
  b3b483fb
25 Feb, 2022 1 commit
- downgraded markupsafe in conda env for jinja · 0d8d99d5
  Eric CHARPENTIER authored Feb 25, 2022
  
  0d8d99d5
31 Jan, 2022 1 commit
- update srp env, advice user to install conda env with mamba · 33a98411
  Eric CHARPENTIER authored Jan 31, 2022
  
  33a98411
07 Jan, 2022 1 commit
- force older version of filelock 3.4.1 since new version 3.4.2 drops support for python 3.6 · b002bce6
  Eric CHARPENTIER authored Jan 07, 2022
  
  b002bce6
14 Sep, 2021 1 commit
- Merge branch 'fix-mamba' into 'master' · 26379c90
  Eric CHARPENTIER authored Sep 14, 2021
```
fix do.db dependency resolution with mamba

See merge request !36
```
  26379c90
10 Sep, 2021 1 commit
- fix do.db dependency resolution with mamba · 63f99917
  Philippe BORDRON authored Sep 10, 2021
  
  63f99917
21 Jun, 2021 1 commit
- updated make_ref to set gene symbol instead of ensg in sym2ref when using ensembl · 9d604c6c
  Eric CHARPENTIER authored Jun 21, 2021
  
  9d604c6c
25 May, 2021 1 commit
- fixed minor bug is samplesheet checking · f5e1eb50
  Eric CHARPENTIER authored May 25, 2021
  
  f5e1eb50
18 May, 2021 2 commits
- changed config_used.json location for multiplates analysis. added triggering... · 319232c2
  Eric CHARPENTIER authored May 18, 2021
```
changed config_used.json location for multiplates analysis. added triggering of tertiary analysis for multiplates.
```
  319232c2
- fixed bug in config2inputs which printed all samples instead of samples in project only · 3e1e42d3
  Eric CHARPENTIER authored May 18, 2021
  
  3e1e42d3
17 May, 2021 1 commit
- fixed bug in snakemake launch for multiplates analysis · b55fce65
  Eric CHARPENTIER authored May 17, 2021
  
  b55fce65
07 Apr, 2021 1 commit
- Add LICENSE · 98c4ce3a
  Audrey BIHOUEE authored Apr 07, 2021
  
  98c4ce3a
06 Apr, 2021 1 commit
- merged all reports into one. Added triggering of functional annotation only... · c7848378
  Eric CHARPENTIER authored Apr 06, 2021
```
merged all reports into one. Added triggering of functional annotation only when databases are defined.
```
  c7848378
12 Mar, 2021 2 commits
- fixed option for univ nantes proxy · fcdbee13
  Eric CHARPENTIER authored Mar 12, 2021
  
  fcdbee13
- added chrM for refseq ref when no chr file is available by downloading the... · 662fcd32
  Eric CHARPENTIER authored Mar 12, 2021
```
added chrM for refseq ref when no chr file is available by downloading the full genome and extracting chrM
```
  662fcd32
10 Mar, 2021 3 commits
- changed logo in reports · ba6cd61e
  Eric CHARPENTIER authored Mar 10, 2021
  
  ba6cd61e
- fixed bug in last commit · cadbb121
  Eric CHARPENTIER authored Mar 10, 2021
  
  cadbb121
- added sample condition and project in getBadSamplesForRun script · 1d96da1a
  Eric CHARPENTIER authored Mar 10, 2021
  
  1d96da1a
25 Feb, 2021 1 commit
- added description for bad samples script · 47638fc7
  Eric CHARPENTIER authored Feb 25, 2021
  
  47638fc7
23 Feb, 2021 3 commits
- fixed small bug in new script · 27e3e4ec
  Eric CHARPENTIER authored Feb 23, 2021
  
  27e3e4ec
- added script to find bad samples in a run · 326a0758
  Eric CHARPENTIER authored Feb 23, 2021
  
  326a0758
- added cow genome. Fixed reading track names for ensembl · caa47e70
  Eric CHARPENTIER authored Feb 23, 2021
  
  caa47e70
29 Jan, 2021 2 commits
- added bostau (cow) refs · db0d99aa
  Eric CHARPENTIER authored Jan 29, 2021
  
  db0d99aa
- added DOI links in report and readme · e361773e
  Eric CHARPENTIER authored Jan 29, 2021
  
  e361773e
26 Jan, 2021 1 commit
- limited threads in split_fastq to avoid out of memory and cores · df6eca84
  Eric CHARPENTIER authored Jan 26, 2021
  
  df6eca84
22 Jan, 2021 1 commit
- fixed bug in make_srp_config script, thx Raluca · 42d67d02
  Eric CHARPENTIER authored Jan 22, 2021
  
  42d67d02
15 Jan, 2021 3 commits
- fixed typo · 58ba6c49
  Eric CHARPENTIER authored Jan 15, 2021
  
  58ba6c49
- updated multiplates readme to take into account the possibility of specifing... · 81b3b65d
  Eric CHARPENTIER authored Jan 15, 2021
```
updated multiplates readme to take into account the possibility of specifing new factors for samples
```
  81b3b65d
- added possibility to define new factors in samplesheet for multiplate analysis · cfaeb19a
  Eric CHARPENTIER authored Jan 15, 2021
  
  cfaeb19a
07 Jan, 2021 1 commit
- added link to reanalyze data · 37e9f750
  Eric CHARPENTIER authored Jan 07, 2021
  
  37e9f750
04 Dec, 2020 1 commit
- added precisions in the multiplates readme · 5b4184e6
  Eric CHARPENTIER authored Dec 04, 2020
  
  5b4184e6
03 Dec, 2020 2 commits
- Merge branch 'master' of https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline · 1838d7cc
  Eric CHARPENTIER authored Dec 03, 2020
  
  1838d7cc
- added possibility to select samples and override conditions by specifying a... · 74c7f5ec
  Eric CHARPENTIER authored Dec 03, 2020
```
added possibility to select samples and override conditions by specifying a samplesheet in the multiplates analysis
```
  74c7f5ec
02 Dec, 2020 3 commits
- Update README.md · 67fb0fb4
  Audrey BIHOUEE authored Dec 02, 2020
  
  67fb0fb4
- Update README.md · 3b29a823
  Audrey BIHOUEE authored Dec 02, 2020
  
  3b29a823
- Update README.md · ae56649b
  Audrey BIHOUEE authored Dec 02, 2020
  
  ae56649b
24 Nov, 2020 1 commit
- fixed bug when scaling with NA values in DEG heatmap · 2b828850
  Eric CHARPENTIER authored Nov 24, 2020
  
  2b828850
18 Nov, 2020 1 commit
- fixed bugs for R4 · 3f119742
  Eric CHARPENTIER authored Nov 18, 2020
  
  3f119742