Commits · test-CI · bird_pipeline_registry / RNAseq-quantif-pipeline

17 Sep, 2020 9 commits
- remove one constraint about snakemake-minimal · 56da2a1e
  vintache-d authored Sep 17, 2020
  
  56da2a1e
- Update executePipeline.sh - test if the file Results/Report/report.html exist · a2272992
  Damien VINTACHE authored Sep 11, 2020
  
  a2272992
- Update executePipeline.sh - remove the md5sum check · a38507a9
  Damien VINTACHE authored Sep 11, 2020
  
  a38507a9
- Update .gitlab-ci.yml - set proxy variable for docker execution · f7b5a4f3
  Damien VINTACHE authored Sep 11, 2020
  
  f7b5a4f3
- Update .gitlab-ci.yml - use only one argument for pipeline execution · 2d9cf2c4
  Damien VINTACHE authored Sep 11, 2020
  
  2d9cf2c4
- use gitlab-ci only for the branch test-CI · d151b483
  vintache-d authored Sep 11, 2020
  
  d151b483
- mise à jour du fichier md5sum · 41a05fc1
  vintache-d authored Sep 11, 2020
  
  41a05fc1
- the version of snakemake-minimal must be lower than 5.23 and greater than 5.2 · 2c2f6969
  vintache-d authored Sep 11, 2020
  
  2c2f6969
- add files for continuous integration with gitlab-ci · f5be7bc5
  vintache-d authored Sep 10, 2020
  
  f5be7bc5
16 Sep, 2020 1 commit
- changed treated condition name. update multiqc to from 1.6 to 1.9 · eb2db90e
  Eric CHARPENTIER authored Sep 16, 2020
  
  eb2db90e
10 Sep, 2020 1 commit
- fix bug · 295821f0
  Eric CHARPENTIER authored Sep 10, 2020
  
  295821f0
27 Aug, 2020 1 commit
- added full deseq2 result table downloas in report · b3d676bd
  Eric CHARPENTIER authored Aug 27, 2020
  
  b3d676bd
26 Aug, 2020 1 commit
- added full deseq2 results table download in report · 168ce09b
  Eric CHARPENTIER authored Aug 26, 2020
  
  168ce09b
24 Aug, 2020 1 commit
- updated library-type specification · 5020dc5a
  Eric CHARPENTIER authored Aug 24, 2020
  
  5020dc5a
22 Jul, 2020 2 commits
- merged Audrey's code · 2abaac55
  Eric CHARPENTIER authored Jul 22, 2020
  
  2abaac55
- added fpkm and tpm counts · 80a239b7
  Eric CHARPENTIER authored Jul 22, 2020
  
  80a239b7
21 Jul, 2020 3 commits
- ajout cible fpkm. Manque bed · 38e6d44f
  Audrey BIHOUEE authored Jul 21, 2020
  
  38e6d44f
- updated readme. Running pipe on test data on one core without cluster mode.... · 8f04370f
  Eric CHARPENTIER authored Jul 21, 2020
```
updated readme. Running pipe on test data on one core without cluster mode. Added new environement withou R packages compilation. Removed install_dependencies
```
  8f04370f
- fixed targets and biomart access. · 20ed0f19
  Eric CHARPENTIER authored Jul 21, 2020
  
  20ed0f19
29 Mar, 2020 1 commit
- modified references.json for bird cluster, modified the way biomart is accessed · 964efc3c
  Eric CHARPENTIER authored Mar 29, 2020
  
  964efc3c
04 Mar, 2020 3 commits
- Update for reference file missing · 2c846eae
  Audrey BIHOUEE authored Mar 04, 2020
  
  2c846eae
- Update for reference file missing · ee894775
  Audrey BIHOUEE authored Mar 04, 2020
  
  ee894775
- Update for reference file missing · 132f1bf2
  Audrey BIHOUEE authored Mar 04, 2020
  
  132f1bf2
02 Mar, 2020 1 commit
- fixed bug when no annot file has been created while creating report · 2a078a20
  Eric CHARPENTIER authored Mar 02, 2020
  
  2a078a20
04 Dec, 2019 11 commits
- report enhance · 8c9ca764
  Eric CHARPENTIER authored Dec 04, 2019
  
  8c9ca764
- fixed creation of report broken in last commit, updated readme · b096ee23
  Eric CHARPENTIER authored Dec 04, 2019
  
  b096ee23
- added check for annotation images in report · acd7143c
  Eric CHARPENTIER authored Dec 04, 2019
  
  acd7143c
- added version script (forgotten for last commit) · f8afb27c
  Eric CHARPENTIER authored Dec 04, 2019
  
  f8afb27c
- added tools versions in report, cleaned scripts · eed677aa
  Eric CHARPENTIER authored Dec 04, 2019
  
  eed677aa
- Merge branch 'refactorcode' into 'master' · b27c68ac
  Eric CHARPENTIER authored Dec 04, 2019
```
merge branch Refactorcode into master

See merge request !3
```
  b27c68ac
- Merge branch 'master' into 'refactorcode' · 6e621059
  Eric CHARPENTIER authored Dec 04, 2019
```
# Conflicts:
#   Snakefile
```
  6e621059
- fixed bug in annotation creation and put back 100 bases length for reads by default · 2d51294e
  Eric CHARPENTIER authored Dec 04, 2019
  
  2d51294e
- added git attributes to remove css, js libs · 3f0f899b
  Eric CHARPENTIER authored Dec 04, 2019
  
  3f0f899b
- checking project name during config file creation · 22845539
  Eric CHARPENTIER authored Dec 04, 2019
  
  22845539
- added read group in bam files · 1e004588
  Eric CHARPENTIER authored Dec 04, 2019
  
  1e004588
29 Nov, 2019 2 commits

Merge branch 'master' into 'master' · c5ceda3f
Eric CHARPENTIER authored Nov 29, 2019
```
Ajout de outSAMattrRGline cf :...

See merge request !2
```
c5ceda3f

Ajout de outSAMattrRGline cf :... · 1f9bfa30

Pierre LINDENBAUM authored Nov 29, 2019

Ajout de outSAMattrRGline cf : http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf 

> string(s):  SAM/BAM read group line.  The first word contains the read groupidentifier and must start with ”ID:”, e.g.  –outSAMattrRGline ID:xxx CN:yy”DS:z z z”.xxx will be added as RG tag to each output alignment.  Any spaces in the tagvalues have to be double quoted

1f9bfa30

18 Nov, 2019 1 commit
- refactored conda envs to create only one · 1ab964e9
  Eric CHARPENTIER authored Nov 18, 2019
  
  1ab964e9
08 Jul, 2019 1 commit
- fixed creation of clustDE output and input when no DEG found 2 - thx atorres · ad4c1c77
  Eric CHARPENTIER authored Jul 08, 2019
  
  ad4c1c77
28 Jun, 2019 1 commit
- updated README with troubleshooting for PS1 unbound variable bug · 441d694b
  Eric CHARPENTIER authored Jun 28, 2019
  
  441d694b