Commits · master · edna / snakemake_rapidrun_obitools

27 Jan, 2023 1 commit
- fix(write_demultiplex_files.py): The first sample of all_samples is now analysed · 7b9c62b6
  mbruno authored Jan 27, 2023
  
  7b9c62b6
16 Dec, 2022 1 commit
- style(config_template): fix typo · d9862088
  mbruno authored Dec 16, 2022
  
  d9862088
15 Dec, 2022 2 commits
- Merge branch 'master' of https://gitlab.mbb.cnrs.fr/edna/snakemake_rapidrun_obitools · 8cf656c9
  mbruno authored Dec 15, 2022
  
  8cf656c9
- fix(clean_pcrerr_samples): fix obiclean error when empty input file · afa6bdad
  mbruno authored Dec 15, 2022
  
  afa6bdad
12 Dec, 2022 3 commits
- fix(obitools_envs): conda env creation too long · ff76f358
  mbruno authored Dec 12, 2022
```
Remove unnecessary dependencies
```
  ff76f358
- refactor(rules, config): rename some subfolders keys · 94f4cc86
  mbruno authored Dec 12, 2022
  
  94f4cc86
- Merge branch 'develop' · 0850232c
  mbruno authored Dec 12, 2022
  
  0850232c
28 Nov, 2022 4 commits
- style(Snakefile): fix typo · c29e8d28
  mbruno authored Nov 28, 2022
  
  c29e8d28
- status(Snakefile): Developement to Production · 35b6acfe
  mbruno authored Nov 28, 2022
  
  35b6acfe
- docs(readme): update Quick Start in README.md · e83de952
  mbruno authored Nov 28, 2022
  
  e83de952
- docs(changelog): update change log with 1.3.0 · 003e371c
  mbruno authored Nov 28, 2022
  
  003e371c
25 Nov, 2022 8 commits
- refactor(config_template): add comment · 23813c47
  mbruno authored Nov 25, 2022
  
  23813c47
- remove(envs/fastqsplitter_envs.yaml): unused conda env · b94ea707
  mbruno authored Nov 25, 2022
  
  b94ea707
- Remove old config files · fbb112f4
  mbruno authored Nov 25, 2022
  
  fbb112f4
- Remove unused rules · bc07ab2c
  mbruno authored Nov 25, 2022
  
  bc07ab2c
- refactor(split_fastq.smk): replace fastqsplitter by seqkit split2 · 93e16435
  mbruno authored Nov 25, 2022
  
  93e16435
- feat: change input and ouptut paths · 06248f49
  mbruno authored Nov 25, 2022
```
- add subfolder keys in config file
- add Path function (from pathlib.py)
```
  06248f49
- style(Snakefile): remove empty lines · 02fb3766
  mbruno authored Nov 25, 2022
  
  02fb3766
- Update README: remove slack link · e0989364
  mbruno authored Nov 25, 2022
```
The slack channel 'metabarcoding_otu' no longer exist.
```
  e0989364
23 Nov, 2022 1 commit
- style(Snakemake): Add comments · 7ccb15bc
  mbruno authored Nov 23, 2022
  
  7ccb15bc
14 Oct, 2022 4 commits
- fix(checkpoint): problem with empty files · 09526b88
  mbruno authored Oct 14, 2022
  
  09526b88
- refactor(table_assigned_sequences.smk): add {projet} and {marker} in output file name · 7154d251
  mbruno authored Oct 14, 2022
  
  7154d251
- fix(ngsfilter.smk): MissingOutputException · 4242a6ce
  mbruno authored Oct 14, 2022
  
  4242a6ce
- fix(ngsfilter.smk): ValueError: malformed node or string · 73c4c39a
  mbruno authored Oct 14, 2022
  
  73c4c39a
09 Sep, 2022 2 commits
- fix(get_targets): no longer returns the same file multiple times · 8c554ae1
  mbruno authored Sep 09, 2022
  
  8c554ae1
- Update samples_to_runs.smk · c6ef807e
  mbruno authored Sep 09, 2022
  
  c6ef807e
06 Sep, 2022 1 commit
- feat(prepare_spygen): create all_samples.csv (required in the config file) · 4a8328ec
  mbruno authored Sep 06, 2022
  
  4a8328ec
05 Sep, 2022 1 commit
- Reverting to cdfa6fca · 865ca8f8
  mbruno authored Sep 05, 2022
  
  865ca8f8
01 Sep, 2022 2 commits
- commom.smk: remove print in get_internal_samples + remove commented function · e3091f67
  mbruno authored Sep 01, 2022
  
  e3091f67
- fix(obisplit.smk): replace rule by checkpoint · 0c58351c
  mbruno authored Sep 01, 2022
```
Relates to #16 and #15
```
  0c58351c
18 Jul, 2022 1 commit
- refactor(chunk_illuminapairend.smk, obisplit.smk): add key 'priority' · 922e421b
  mbruno authored Jul 18, 2022
  
  922e421b
12 Jul, 2022 1 commit
- fix(split_fastq.smk): change output · 32e6a86c
  mbruno authored Jul 12, 2022
```
Relates to #15
```
  32e6a86c
01 Apr, 2022 3 commits

ci(obisplit): add resources bigfile · 8b6b54da

mbruno authored Apr 01, 2022

Related to https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/5 and https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/12

8b6b54da

Merge branch 'develop' of... · 60d83b52

mbruno authored Apr 01, 2022

Merge branch 'develop' of https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools into develop

60d83b52

ci(goodlength_samples): add parameter priority · 811d7f2d

mbruno authored Apr 01, 2022

Force rule goodlength_samples execution over all rules
Related to https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/5 and https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/12

811d7f2d

21 Feb, 2022 3 commits
- Update config_template.yaml · 3f1c6ded
  mbruno authored Feb 21, 2022
  
  3f1c6ded
- Update config_template.yaml · 5219a389
  mbruno authored Feb 21, 2022
  
  5219a389
- Update config_template.yaml · a5cb0730
  mbruno authored Feb 21, 2022
  
  a5cb0730
15 Feb, 2022 1 commit
- fix(write_demultiplex_files.py): correct minor typo in code · ee5cd976
  mbruno authored Feb 15, 2022
  
  ee5cd976
14 Feb, 2022 1 commit
- refactor(config): add a config file template · 968582ee
  mbruno authored Feb 14, 2022
  
  968582ee