Commits · master · Metagenomics / snakemake

16 Aug, 2021 1 commit
- Merge branch '32-unmapped-reads' into 'master' · 0669a295
  Kenzo-Hugo Hillion authored Aug 16, 2021
```
Resolve "get unmapped reads"

Closes #32

See merge request !7
```
  0669a295
13 Aug, 2021 1 commit
- bamtofastq pairs · bb2d822a
  Kenzo-Hugo Hillion authored Aug 13, 2021
  
  bb2d822a
09 Aug, 2021 1 commit
- fix bamtofastq_pairs · 60b2f40e
  Kenzo-Hugo Hillion authored Aug 09, 2021
  
  60b2f40e
02 Aug, 2021 2 commits
- start bedtools bamtofastq · 93e24e41
  Kenzo-Hugo Hillion authored Aug 02, 2021
  
  93e24e41
- update extract of unmapped pairs with samtools · 1998065a
  Kenzo-Hugo Hillion authored Aug 02, 2021
  
  1998065a
30 Jul, 2021 1 commit
- example for extracting unmapped pairs · bca19306
  Kenzo-Hugo Hillion authored Jul 30, 2021
  
  bca19306
28 Jul, 2021 1 commit
- start Snakefile to extract unmapped pairs · c7cb5e46
  Kenzo-Hugo Hillion authored Jul 28, 2021
  
  c7cb5e46
20 Jul, 2021 2 commits
- start snakemake for samtools view · deffb1dd
  Kenzo-Hugo Hillion authored Jul 20, 2021
  
  deffb1dd
- file rights · 05042bc7
  Kenzo-Hugo Hillion authored Jul 20, 2021
  
  05042bc7
29 Dec, 2020 2 commits
- Merge branch '21-metaphlan3' into 'master' · cca807a5
  Kenzo-Hugo Hillion authored Dec 29, 2020
```
update metaphlan3 and add strainphlan

Closes #22

See merge request !6
```
  cca807a5
- add workflow for strainphlan on paired-end · 38125af0
  Kenzo-Hugo Hillion authored Dec 29, 2020
  
  38125af0
18 Dec, 2020 1 commit
- add rule for strainphlan · bd2e900e
  Kenzo-Hugo Hillion authored Dec 18, 2020
  
  bd2e900e
14 Dec, 2020 4 commits
- start structure for strainphlan tools · 6e60eb18
  Kenzo-Hugo Hillion authored Dec 14, 2020
  
  6e60eb18
- update paths from tars to maestro · 8a7ec2e8
  Kenzo-Hugo Hillion authored Dec 14, 2020
  
  8a7ec2e8
- update README.md · 14ff6d94
  Kenzo-Hugo Hillion authored Dec 14, 2020
  
  14ff6d94
- update metaphlan3 pipeline · 17767e09
  Kenzo-Hugo Hillion authored Dec 14, 2020
  
  17767e09
10 Dec, 2020 1 commit
- Merge branch '21-metaphlan3' into 'master' · 18caac99
  Kenzo-Hugo Hillion authored Dec 10, 2020
```
metaphlan3 and strainphlan

Closes #21

See merge request !5
```
  18caac99
19 Nov, 2020 8 commits
- mv output dir to params · b265ed7f
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  b265ed7f
- add sample2markers for strainphlan · 3bd54e46
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  3bd54e46
- update paired metaphlan with new outputs · e60c44c9
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  e60c44c9
- move bowtie2out and sams from params to output · 6cad6524
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  6cad6524
- add sams output to paired metaphlan · 0ddcffa4
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  0ddcffa4
- fix Snakefile · d1e501f6
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  d1e501f6
- add sams output from metaphlan3 · 491d5f1c
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  491d5f1c
- start metaphlan3 rules · 4134975f
  Kenzo-Hugo Hillion authored Nov 19, 2020
  
  4134975f
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