Commits · a4180b4727910118633c2116f2c66b747d7df821 · Sam Nooij / Jovian screener

30 Jun, 2020 2 commits
- Fix bug with reading scaffolds files from sample sheet · a4180b47
  Sam Nooij authored Jun 30, 2020
  
  a4180b47
- Fix bug with reading reads files from sample sheet · 22b46175
  Sam Nooij authored Jun 30, 2020
  
  22b46175
26 Jun, 2020 1 commit
- Update README.md · ce51c184
  Sam Nooij authored Jun 26, 2020
  
  ce51c184
24 Jun, 2020 1 commit
- Remove unnecessary whitespaces · 84041347
  Sam Nooij authored Jun 24, 2020
  
  84041347
23 Jun, 2020 4 commits
- Correct conda env name · 9773f70d
  Sam Nooij authored Jun 23, 2020
  
  9773f70d
- Change sample_sheet to lowercase · 4a95784d
  Sam Nooij authored Jun 23, 2020
  
  4a95784d
- Create data directory if it does not exist · 559e0b40
  Sam Nooij authored Jun 23, 2020
  
  559e0b40
- Add download instruction · bfab2219
  Sam Nooij authored Jun 23, 2020
  
  bfab2219
07 Apr, 2020 2 commits
- Correct typo: default samples value · 576359c1
  Sam Nooij authored Apr 07, 2020
  
  576359c1
- Correct typo in comment · 0c50ad5c
  Sam Nooij authored Apr 07, 2020
  
  0c50ad5c
01 Apr, 2020 1 commit
- Add missing column name to empty output file · 18fdb396
  Sam Nooij authored Apr 01, 2020
  
  18fdb396
27 Mar, 2020 9 commits
- Make pyANI use threads from config · dd5e01c5
  Sam Nooij authored Mar 27, 2020
  
  dd5e01c5
- Add missing hashtag for link · 496c96e8
  Sam Nooij authored Mar 27, 2020
  
  496c96e8
- Add content list · dae0d302
  Sam Nooij authored Mar 27, 2020
  
  dae0d302
- Add note on --keep-going when pyANI might fail · d61c2a8c
  Sam Nooij authored Mar 27, 2020
  
  d61c2a8c
- Merge branch 'pyani' into 'master' · 767dde15
  Sam Nooij authored Mar 27, 2020
```
Correct pyANI species comparison rule

See merge request !1
```
  767dde15
- Add bwa-samtools env file · 8d845c28
  Sam Nooij authored Mar 27, 2020
  
  8d845c28
- Correct pyANI species comparison rule · 4262e599
  Sam Nooij authored Mar 27, 2020
  
  4262e599
- Add compare_species_fastas · e9f65315
  Sam Nooij authored Mar 27, 2020
  
  e9f65315
- Add tax_name to quantified Blast output · 65c811f1
  Sam Nooij authored Mar 27, 2020
  
  65c811f1
26 Mar, 2020 20 commits
- Correct inconsistent variable names · e06e2b53
  Sam Nooij authored Mar 26, 2020
  
  e06e2b53
- Add WIP badge · 507f1a87
  Sam Nooij authored Mar 26, 2020
  
  507f1a87
- Improve onsuccess cleaning · c9a9b5b6
  Sam Nooij authored Mar 26, 2020
  
  c9a9b5b6
- Solve issues with Path · ef0ee237
  Sam Nooij authored Mar 26, 2020
  
  ef0ee237
- Add exception for empty blast file · dcc5b5d3
  Sam Nooij authored Mar 26, 2020
  
  dcc5b5d3
- Solve error with column names by join method · 632967ef
  Sam Nooij authored Mar 26, 2020
  
  632967ef
- Undo rename file that breaks snakemake · bf68d8af
  Sam Nooij authored Mar 26, 2020
  
  bf68d8af
- Change intermediate directory to data/tmp (solve #2 ) · 088c3456
  Sam Nooij authored Mar 26, 2020
  
  088c3456
- Parse sequence legths with Biopython (solve #1 ) · 11e11da4
  Sam Nooij authored Mar 26, 2020
  
  11e11da4
- Sum paired and unpaired depth of coverage · 0a7cf90a
  Sam Nooij authored Mar 26, 2020
  
  0a7cf90a
- Merge branch 'master' of git.lumc.nl:snooij/jovian-screener · 6cc75202
  Sam Nooij authored Mar 26, 2020
  
  6cc75202
- Fix accidental overwriting of 'Reference' column · 9173321e
  Sam Nooij authored Mar 26, 2020
  
  9173321e
- Fix accidental overwriting of 'Reference' column · 14b5a66f
  Sam Nooij authored Mar 26, 2020
  
  14b5a66f
- Change sum rule to script · 2b86acc8
  Sam Nooij authored Mar 26, 2020
```
because it is impossible to use conda environments with snakemake's run
```
  2b86acc8
- Sum paired and unpaired mapped reads · 842bde2d
  Sam Nooij authored Mar 26, 2020
  
  842bde2d
- Concatenate depth of coverage tables · f0bb09fb
  Sam Nooij authored Mar 26, 2020
  
  f0bb09fb
- Remove path from filename · b8bd22fc
  Sam Nooij authored Mar 26, 2020
  
  b8bd22fc
- Remove (un)paired from reference name · baa71e65
  Sam Nooij authored Mar 26, 2020
  
  baa71e65
- Concatenate per sample mapped read counts · 61595ce2
  Sam Nooij authored Mar 26, 2020
  
  61595ce2
- Add whitespace to correct printed message · ed0b9149
  Sam Nooij authored Mar 26, 2020
  
  ed0b9149