Commits · squeezemeta · mmassaviol / WAWmassaviol

28 Oct, 2021 6 commits
- Merge branch 'master' into squeezemeta · c6dc214c
  abensaid authored Oct 28, 2021
  
  c6dc214c
- change json dir · ff3a400d
  khalid authored Oct 28, 2021
  
  ff3a400d
- Add bedtools and test for gff in Radsex map report · 08afc43e
  khalid authored Oct 28, 2021
  
  08afc43e
- Now save workflow json in results dir after run · 39378446
  khalid authored Oct 28, 2021
  
  39378446
- Deal with cases where groups are numbers · 12d21101
  khalid authored Oct 28, 2021
  
  12d21101
- Now save workflow json in results dir after run · e027e21a
  khalid authored Oct 28, 2021
  
  e027e21a
26 Oct, 2021 3 commits
- bug in sorting popmap · 3f2762e4
  khalid authored Oct 26, 2021
  
  3f2762e4
- Test if results dir exists · f00f308a
  khalid authored Oct 26, 2021
  
  f00f308a
- deal with results dir containing minus hyphen · 7e6b7edb
  khalid authored Oct 26, 2021
  
  7e6b7edb
25 Oct, 2021 2 commits
- better handling of raw counts file in deseq2 · 61a794ee
  khalid authored Oct 25, 2021
  
  61a794ee
- deseq Top genes changes · dd513a7d
  khalid authored Oct 25, 2021
  
  dd513a7d
22 Oct, 2021 2 commits
- Change species names for deseq · c53fda77
  khalid authored Oct 22, 2021
  
  c53fda77
- debug trimmomatic SE · 66e44bdb
  khalid authored Oct 22, 2021
  
  66e44bdb
21 Oct, 2021 6 commits
- dupliacted param in Trimmomatic · 606dfdd4
  khalid authored Oct 21, 2021
  
  606dfdd4
- docker_base is a newer ubuntu distrib. with R 4.1 · c2c67d59
  khalid authored Oct 21, 2021
  
  c2c67d59
- fix trimmomatic_SE output name · 45008375
  khalid authored Oct 21, 2021
  
  45008375
- trimmomatic_otherparams for SE and PE · 2c7ec357
  khalid authored Oct 21, 2021
  
  2c7ec357
- Add a helper script to run on a SGE cluster · e4438c46
  khalid authored Oct 21, 2021
  
  e4438c46
- Generate a Singularity.def file · 9cdc0990
  khalid authored Oct 21, 2021
  
  9cdc0990
20 Oct, 2021 2 commits
- Show absolute path to results in multiqc report · 1fe90db5
  khalid authored Oct 20, 2021
  
  1fe90db5
- Show mismach in blastn results · 4637e3ab
  khalid authored Oct 20, 2021
  
  4637e3ab
19 Oct, 2021 3 commits
- Set minAdapterLength to 0 for Trimmomatic · d3b34b20
  khalid authored Oct 19, 2021
  
  d3b34b20
- Add a way to refresh multiqc_report to override navigator cache · 23bf0b19
  khalid authored Oct 19, 2021
  
  23bf0b19
- Force Report memo to be a string · 4d6d899e
  khalid authored Oct 19, 2021
  
  4d6d899e
18 Oct, 2021 2 commits
- Add annotation file to rasex_map and changes to Trimmomatic · 7445c578
  khalid authored Oct 18, 2021
  
  7445c578
- Merge branch 'master' into squeezemeta · 4a706151
  abensaid authored Oct 18, 2021
  
  4a706151
15 Oct, 2021 4 commits
- Add raw hisat2_index · 7cd140c9
  khalid authored Oct 15, 2021
  
  7cd140c9
- Add raw hisat2_index · 3e27cabb
  khalid authored Oct 15, 2021
  
  3e27cabb
- hisat2 typos · c1fd5d10
  khalid authored Oct 15, 2021
  
  c1fd5d10
- check if reads are genomic or Rna before calling hisat2 with pair-end params · 62723ea1
  khalid authored Oct 15, 2021
  
  62723ea1
14 Oct, 2021 4 commits
- Merge branch 'master' into squeezemeta · 95617d8a
  abensaid authored Oct 14, 2021
  
  95617d8a
- fastp report title · 82a1e0c1
  khalid authored Oct 14, 2021
  
  82a1e0c1
- Fastqc now declared output is only a logfile · cb384fe6
  khalid authored Oct 14, 2021
  
  cb384fe6
- Fastqc now declared output is only a logfile · d7e0ddfe
  khalid authored Oct 14, 2021
  
  d7e0ddfe
13 Oct, 2021 6 commits
- debug fastp · f2c99462
  khalid authored Oct 13, 2021
  
  f2c99462
- debug fastp · 14182ee0
  khalid authored Oct 13, 2021
  
  14182ee0
- debug fastp · d80d8daa
  khalid authored Oct 13, 2021
  
  d80d8daa
- Add fastp PE adapter detection and change json file name to allow MultiQC detection · 81756677
  khalid authored Oct 13, 2021
  
  81756677
- New version of fastp · edfc3cd5
  khalid authored Oct 13, 2021
  
  edfc3cd5
- Add a PE_Mark variable for pair-end raw_reads · afd4bd7c
  khalid authored Oct 13, 2021
  
  afd4bd7c