Commits · 8f50b748ab0d07d34e00cb81c658ef9ce8263043 · GUDMAP_RBK / RNA-seq

Mar 02, 2021
- Fix seqwho tsv output for multiqc · 8f50b748
  Gervaise Henry authored 4 years ago
  
  8f50b748
- Add seqwho infer QC table to multiqc · d1271604
  Gervaise Henry authored 4 years ago
  
  d1271604
Feb 24, 2021
- Move nf and confs to match nextflow format · f8eeebc2
  Gervaise Henry authored 4 years ago
  
  f8eeebc2
Feb 23, 2021
- Replace species inference with seqwho · 634fd8a3
  Gervaise Henry authored 4 years ago
  
  634fd8a3
Feb 19, 2021
- Move non nextflow configs back to workflow and symlink files · 4bd19e37
  Gervaise Henry authored 4 years ago
  
  4bd19e37
Feb 11, 2021
- Nextflow-ify · 0a4b00a6
  Gervaise Henry authored 4 years ago
  
  0a4b00a6
Feb 10, 2021
- Add local configs · 76775df8
  Gervaise Henry authored 4 years ago
  
  76775df8
Feb 09, 2021
- Add dnanexus configs · ec4e0c7e
  Gervaise Henry authored 4 years ago
  
  ec4e0c7e
- Start implementing seqwho · 34803354
  Gervaise Henry authored 4 years ago
  
  34803354
Jan 25, 2021
- Merge data error pre-Execution run · 77410b76
  Gervaise Henry authored 4 years ago
  
  77410b76
- Add blank mRNA_QC on data fail · f4e88555
  Gervaise Henry authored 4 years ago
  
  f4e88555
- Update Has_Strand_Specific_Information to Strandedness · 3b3b7891
  Gervaise Henry authored 4 years ago
  
  3b3b7891
- Update Sequencing_Type to Experiment_Type · a5aedff5
  Gervaise Henry authored 4 years ago
  
  a5aedff5
Jan 20, 2021
- Make sampled align use > 32GB nodes on BioHPC · 9e121dac
  Gervaise Henry authored 4 years ago
  
  9e121dac
- Add premature fail execution run upload with fastq file error · 94dac4ed
  Gervaise Henry authored 4 years ago
  
  94dac4ed
Jan 19, 2021
- Filter input bag export config to only get fastq's matching convention · 5d9c691f
  Gervaise Henry authored 4 years ago
  
  5d9c691f
Jan 15, 2021
- Add in missinng process config. · fa009e23
  Venkat Malladi authored 4 years ago
  
  fa009e23
- Update biohpc.config · 73490420
  Venkat Malladi authored 4 years ago
  
  73490420
- Update aws.config · bce79412
  Venkat Malladi authored 4 years ago
  
  bce79412
Jan 08, 2021
- Fix time param · 57423462
  Gervaise Henry authored 4 years ago
  
  57423462
- Add 4hr time limit for all processes (biohpc.config) · a57f7e87
  Gervaise Henry authored 4 years ago
  
  a57f7e87
- Add 1 retry to all processes · e2773496
  Gervaise Henry authored 4 years ago
  
  e2773496
Jan 07, 2021
- Add retries to all data-hub processes for biohpc config · 2d9e2523
  Gervaise Henry authored 4 years ago
  
  2d9e2523
- Move test inputBag export config to test-data · cb8b218d
  Gervaise Henry authored 4 years ago
  
  cb8b218d
Jan 06, 2021
- Make new inputBag for testing with txt fetch instead of fastq · a2cbcce1
  Gervaise Henry authored 4 years ago
  
  a2cbcce1
- Fix species error variable · 6269b5af
  Gervaise Henry authored 4 years ago
  
  6269b5af
Jan 05, 2021
- Alow 1 retry of getData and trimData · 02d4766e
  Gervaise Henry authored 4 years ago
  
  02d4766e
- Fix fail pre execution run · 52b950a6
  Gervaise Henry authored 4 years ago
  
  52b950a6
- Use larger nodes for trim process · a1127c20
  Gervaise Henry authored 4 years ago
  
  a1127c20
Jan 04, 2021
- Add fail process to configs · 68acfa31
  Gervaise Henry authored 4 years ago
  
  68acfa31
Jan 03, 2021
- Add finalize execution run and add new references using bag · 57834f48
  Gervaise Henry authored 4 years ago
  
  57834f48
Dec 29, 2020
- Fix multiqc config for updated version · c6e7db5a
  Gervaise Henry authored 4 years ago
  
  c6e7db5a
Dec 17, 2020
- Change process output bag name to uploadProcessedFiles · b08a7fc5
  Gervaise Henry authored 4 years ago
  
  b08a7fc5
- Update replicate bdbag export config name · 17962772
  Gervaise Henry authored 4 years ago
  
  17962772
- Start changing model · 8792bf4b
  Gervaise Henry authored 4 years ago
  
  8792bf4b
Dec 14, 2020
- Add Output Bag · bdfd5567
  Gervaise Henry authored 4 years ago
  
  bdfd5567
Dec 07, 2020
- Add upload output bag · ab0e4bb6
  Gervaise Henry authored 4 years ago
  
  ab0e4bb6
Dec 05, 2020
- Add upload mRNA QC · e4b99530
  Gervaise Henry authored 4 years ago
  
  e4b99530
Dec 02, 2020
- Add upload execution run · 62790800
  Gervaise Henry authored 4 years ago
  
  62790800
Nov 30, 2020
- Add uploadInputBag · eb83dee4
  Gervaise Henry authored 4 years ago
  
  eb83dee4