Commits · master · Metagenomics / snakemake

18 Mar, 2020 2 commits
- Merge branch '16-diamond-through-eggnog-mapper' into 'master' · 8932d738
  Kenzo-Hugo Hillion authored Mar 18, 2020
```
add rule for diamond through eggnogmapper2

Closes #19, #18, #17, and #16

See merge request !4
```
  8932d738
- add workflow for eggnogmapperv2 on large file · 2fda3282
  Kenzo-Hugo Hillion authored Mar 18, 2020
  
  2fda3282
17 Mar, 2020 1 commit
- Start README for workflow · 0462c446
  Kenzo-Hugo Hillion authored Mar 17, 2020
  
  0462c446
16 Mar, 2020 5 commits
- Start rules for annotation with eggnogmapper2 · a959cec8
  Kenzo-Hugo Hillion authored Mar 16, 2020
  
  a959cec8
- fix diamond rule · 22379bcc
  Kenzo-Hugo Hillion authored Mar 16, 2020
  
  22379bcc
- update name in example · a9f73d2f
  Kenzo-Hugo Hillion authored Mar 16, 2020
  
  a9f73d2f
- Merge branch 'master' of gitlab.pasteur.fr:metagenomics/snakemake into... · cf63a929
  Kenzo-Hugo Hillion authored Mar 16, 2020
```
Merge branch 'master' of gitlab.pasteur.fr:metagenomics/snakemake into 16-diamond-through-eggnog-mapper
```
  cf63a929
- starting cat · 93eb643b
  Kenzo-Hugo Hillion authored Mar 16, 2020
  
  93eb643b
13 Mar, 2020 1 commit
- add rule for diamond through eggnogmapper2 · d57802de
  Kenzo-Hugo Hillion authored Mar 13, 2020
  
  d57802de
20 Feb, 2020 2 commits
- Merge branch 'hmenager-master-patch-18814' into 'master' · 2d13178c
  Kenzo-Hugo Hillion authored Feb 20, 2020
```
first draft for a workflow-index description of the single-end metaphlan workflow

See merge request !3
```
  2d13178c
- Update .workflow-index.yml · da8c54e1
  Hervé MENAGER authored Feb 20, 2020
  
  da8c54e1
11 Feb, 2020 3 commits
- Merge branch '15-split-fasta-chunks' into 'master' · ddb68576
  Kenzo-Hugo Hillion authored Feb 11, 2020
```
Split a FASTA file in chunks

Closes #15

See merge request !2
```
  ddb68576
- remove empty file · ec6df182
  Kenzo-Hugo Hillion authored Feb 11, 2020
  
  ec6df182
- finish Snakefile for splitting Fasta · 8c7edff7
  Kenzo-Hugo Hillion authored Feb 11, 2020
  
  8c7edff7
10 Feb, 2020 1 commit
- start Snakefile to split fasta · 2c621522
  Kenzo-Hugo Hillion authored Feb 10, 2020
  
  2c621522
26 Jul, 2019 3 commits
- fix typo dendrogram · e3b2c07b
  Kenzo-Hugo Hillion authored Jul 26, 2019
  
  e3b2c07b
- Merge branch '14-metaphlan2-paired' into 'master' · f485ebed
  Kenzo-Hugo Hillion authored Jul 26, 2019
```
Metaphlan2 to use paired-end reads

Closes #14

See merge request !1
```
  f485ebed
- Metaphlan2 to use paired-end reads · b44971f1
  Kenzo-Hugo Hillion authored Jul 26, 2019
  
  b44971f1
23 Jul, 2019 1 commit
- fix metaphlan2 workflow · 727b51e0
  Kenzo-Hugo Hillion authored Jul 23, 2019
  
  727b51e0
16 May, 2019 3 commits
- add module dependency for graphlan · ba3a4101
  Kenzo-Hugo Hillion authored May 16, 2019
  
  ba3a4101
- fix way to build command line · f2052487
  Kenzo-Hugo Hillion authored May 16, 2019
  
  f2052487
- add possibility to add modules dependencies · bc228c62
  Kenzo-Hugo Hillion authored May 16, 2019
  
  bc228c62
14 May, 2019 3 commits
- update title · 233ca151
  Kenzo-Hugo Hillion authored May 14, 2019
  
  233ca151
- update relative repo path · 164333d6
  Kenzo-Hugo Hillion authored May 14, 2019
  
  164333d6
- update documentation and best practices · 3a4ec78c
  Kenzo-Hugo Hillion authored May 14, 2019
  
  3a4ec78c
13 May, 2019 11 commits
- fix typo in Snakefiles · 7af20a4c
  Kenzo-Hugo Hillion authored May 13, 2019
  
  7af20a4c
- typo snakemake · 7f3a14c9
  Kenzo-Hugo Hillion authored May 13, 2019
  
  7f3a14c9
- fix relative path · 1d152b70
  Kenzo-Hugo Hillion authored May 13, 2019
  
  1d152b70
- fix relative paths to tools Snakefile · 25277f2d
  Kenzo-Hugo Hillion authored May 13, 2019
  
  25277f2d
- fix Snakefile names · 52c704d8
  Kenzo-Hugo Hillion authored May 13, 2019
  
  52c704d8
- rename all as SnakeFile · 9b5fbe32
  Kenzo-Hugo Hillion authored May 13, 2019
  
  9b5fbe32
- add possibility to change ref path to rules in config files · 34ac04e2
  Kenzo-Hugo Hillion authored May 13, 2019
  
  34ac04e2
- add graphlan to metaphlan2 workflow · 8bb596da
  Kenzo-Hugo Hillion authored May 13, 2019
  
  8bb596da
- add subworkflow part and subworkflow metaphlan to graphlan · 8c192e82
  Kenzo-Hugo Hillion authored May 13, 2019
  
  8c192e82
- add rules for graphlan · 2462bf79
  Kenzo-Hugo Hillion authored May 13, 2019
  
  2462bf79
- update README for tools · 43f4ae31
  Kenzo-Hugo Hillion authored May 13, 2019
  
  43f4ae31
10 May, 2019 2 commits
- continue README for tool descriptions · 7d24d76f
  Kenzo-Hugo Hillion authored May 10, 2019
  
  7d24d76f
- start Documentation for Snakemake tools · a7e1c446
  Kenzo-Hugo Hillion authored May 10, 2019
  
  a7e1c446
09 May, 2019 2 commits
- add information about the way of writing workflow · 73abde0f
  Kenzo-Hugo Hillion authored May 09, 2019
  
  73abde0f
- add example of workflow for metaphlan2 · 11a919a4
  Kenzo-Hugo Hillion authored May 09, 2019
  
  11a919a4