Commits · e054c55d9854f08febc3590990494fb19284b7b8 · genotoul-bioinfo / metagWGS

30 Nov, 2021 3 commits
- add expected processes · e054c55d
  Celine Noirot authored Nov 30, 2021
  
  e054c55d
- Merge branch 'dsl1' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 1768834b
  Celine Noirot authored Nov 30, 2021
```
Conflicts:
	main_dsl2.nf
```
  1768834b
- functionnal test · 48fcae48
  Celine Noirot authored Nov 30, 2021
  
  48fcae48
29 Nov, 2021 6 commits
- chunk assembly 10000 · c45313e5
  MARTIN Pierre authored Nov 29, 2021
  
  c45313e5
- changed main_dsl2.nf to main.nf · af5e50ae
  MARTIN Pierre authored Nov 29, 2021
  
  af5e50ae
- clean bin/ folder and update docs for DSL2 · c834610c
  MARTIN Pierre authored Nov 29, 2021
  
  c834610c
- changes to doc · a1d60a1b
  MARTIN Pierre authored Nov 29, 2021
  
  a1d60a1b
- use type of the gene to name the gene. ie CDS, rRNA, tRNA... instead of using Prot_ everywhere · 9fc3c1f2
  Jean Mainguy authored Nov 29, 2021
  
  9fc3c1f2
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 55ac9ea6
  Jean Mainguy authored Nov 29, 2021
  
  55ac9ea6
25 Nov, 2021 3 commits
- fix contigs and reads · d68ad414
  MARTIN Pierre authored Nov 25, 2021
  
  d68ad414
- fixed channel contigs_and_reads in shared.nf to work for HiFi and SR · 30a9cebc
  MARTIN Pierre authored Nov 25, 2021
  
  30a9cebc
- fixed functional test for skips · e3547d79
  MARTIN Pierre authored Nov 25, 2021
  
  e3547d79
19 Nov, 2021 4 commits
- Correct entry of alignment · 76ec529a
  Celine Noirot authored Nov 19, 2021
  
  76ec529a
- merge with my stash · 9e16972d
  Celine Noirot authored Nov 19, 2021
  
  9e16972d
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 0befb1d3
  MARTIN Pierre authored Nov 19, 2021
  
  0befb1d3
- changed skips behaviour to be stop_at_STEP instead of skip_STEP; kept... · cabcc538
  MARTIN Pierre authored Nov 19, 2021
```
changed skips behaviour to be stop_at_STEP instead of skip_STEP; kept skip_STEP behaviour for some optional processes and steps (01, 03, 06 and 07)
```
  cabcc538
18 Nov, 2021 3 commits
- add processes steps · 05b7083d
  Celine Noirot authored Nov 18, 2021
  
  05b7083d
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · e47eb5b7
  MARTIN Pierre authored Nov 18, 2021
  
  e47eb5b7
- Fix to assembly filter to sort files in entry and ensure reproductibility · 99c5e12a
  MARTIN Pierre authored Nov 18, 2021
  
  99c5e12a
15 Nov, 2021 3 commits
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 20c951ba
  Celine Noirot authored Nov 15, 2021
  
  20c951ba
- Remove download of PFAM fix #108 · 0007a2ce
  Celine Noirot authored Nov 15, 2021
  
  0007a2ce
- remove U mode because it is deprecated · 235aac84
  Jean Mainguy authored Nov 15, 2021
  
  235aac84
08 Nov, 2021 6 commits
- changes to database for host index · 87fb8f0e
  MARTIN Pierre authored Nov 08, 2021
  
  87fb8f0e
- changes to database for host index · 62ca01bd
  MARTIN Pierre authored Nov 08, 2021
  
  62ca01bd
- add diamond control parameters · d8d2e624
  Celine Noirot authored Nov 08, 2021
  
  d8d2e624
- Remove Mosdepth · 48c7a16e
  Celine Noirot authored Nov 08, 2021
  
  48c7a16e
- Add skip_clean if type=HiFi to avoid db download · 30233108
  Celine Noirot authored Nov 08, 2021
```
Add check SR parameters
```
  30233108
- keep only primary aln in Hifi read alignment module · 26537612
  Jean Mainguy authored Nov 08, 2021
  
  26537612
05 Nov, 2021 1 commit
- debug samplesheet for HiFi · 86bf1d97
  Jean Mainguy authored Nov 05, 2021
  
  86bf1d97
04 Nov, 2021 2 commits
- Add help and check sample sheet. · 603c3078
  Celine Noirot authored Nov 04, 2021
  
  603c3078
- fixed dedup reads not used · e0dc1b82
  MARTIN Pierre authored Nov 04, 2021
  
  e0dc1b82
01 Nov, 2021 1 commit
- rename diamond_parser to assign_taxo and replace mosdepth by samtools coverage · 4574c94f
  Jean Mainguy authored Nov 01, 2021
  
  4574c94f
28 Oct, 2021 8 commits
- short reads + shared ; all steps done · f7120d09
  MARTIN Pierre authored Oct 28, 2021
  
  f7120d09
- remove trash files · 85ada5d4
  MARTIN Pierre authored Oct 28, 2021
  
  85ada5d4
- fusion · c2f89a05
  MARTIN Pierre authored Oct 28, 2021
  
  c2f89a05
- various fixes · 16d68e81
  MARTIN Pierre authored Oct 28, 2021
  
  16d68e81
- typo · b8683852
  Celine Noirot authored Oct 28, 2021
  
  b8683852
- Debug as we add header in m8 format · 6643c485
  Celine Noirot authored Oct 28, 2021
  
  6643c485
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · dbde0796
  MARTIN Pierre authored Oct 28, 2021
  
  dbde0796
- various fixes to kaiju db · afde3905
  MARTIN Pierre authored Oct 28, 2021
  
  afde3905