Seqwho (!71) · Merge requests · GUDMAP_RBK / RNA-seq

Merged Seqwho

seqwho into develop

Merged Gervaise Henry requested to merge seqwho into develop 4 years ago

Mar 05, 2021
- Fix number order for references.md · eba289dc
  Gervaise Henry authored 4 years ago
  
  eba289dc
Mar 04, 2021
- Fix nextflow.config reference for badges · 1d7acf24
  Gervaise Henry authored 4 years ago
  
  1d7acf24
- Allow uploadExexutionRun to happen with pipeline error(metadata match) · 01aaef87
  Gervaise Henry authored 4 years ago
  
  01aaef87
- Update DAG · f9de49f2
  Gervaise Henry authored 4 years ago
  
  f9de49f2
Mar 03, 2021
- Fix when's · 5a8a4eb0
  Gervaise Henry authored 4 years ago
  
  5a8a4eb0
- Remove species error ci · 0b1a56ba
  Gervaise Henry authored 4 years ago
  
  0b1a56ba
- Remove species error ci · 915684d8
  Gervaise Henry authored 4 years ago
  
  915684d8
- Fix uploadQC_fail input · 4034d0f9
  Gervaise Henry authored 4 years ago
  
  4034d0f9
- Change ci fail ambiguous species to species error · bb8b6af8
  Gervaise Henry authored 4 years ago
  
  bb8b6af8
- Update dag · 8d715996
  Gervaise Henry authored 4 years ago
  
  8d715996
- Update readme · 8ae466dd
  Gervaise Henry authored 4 years ago
  
  8ae466dd
- Update versions · dd503660
  Gervaise Henry authored 4 years ago
  
  dd503660
- Fix versions · 6b685bca
  Gervaise Henry authored 4 years ago
  
  6b685bca
- Split version lines · e2ac42c7
  Gervaise Henry authored 4 years ago
  
  e2ac42c7
Mar 02, 2021
- Fix ci · e43e60c0
  Gervaise Henry authored 4 years ago
  
  e43e60c0
- Not stop after the first 3 images · a087bb4e
  Gervaise Henry authored 4 years ago
  
  a087bb4e
- Not stop after the first 3 images · ef4541cb
  Gervaise Henry authored 4 years ago
  
  ef4541cb
- Not stop after the first 3 images · ededb6d0
  Gervaise Henry authored 4 years ago
  
  ededb6d0
- Only singularity pull 3 containers at a time · fe84267a
  Gervaise Henry authored 4 years ago
  
  fe84267a
- Only singularity pull 5 containers at a time · c59b5eb4
  Gervaise Henry authored 4 years ago
  
  c59b5eb4
- Make cache dir at start of ci · aa955a65
  Gervaise Henry authored 4 years ago
  
  aa955a65
- Fix cache folder · 59dc53b1
  Gervaise Henry authored 4 years ago
  
  59dc53b1
- Fix cache folder · 45c4c7ac
  Gervaise Henry authored 4 years ago
  
  45c4c7ac
- Try to fix cache dir · d1fd2bec
  Gervaise Henry authored 4 years ago
  
  d1fd2bec
- Remove chmod · 8e0c03c1
  Gervaise Henry authored 4 years ago
  
  8e0c03c1
- Try to set restrictive permissions for cache · bfcce8cb
  Gervaise Henry authored 4 years ago
  
  bfcce8cb
- Set permissions for cached dir · 9aa7927c
  Gervaise Henry authored 4 years ago
  
  9aa7927c
- chmod 775 cached images · d9f5e341
  Gervaise Henry authored 4 years ago
  
  d9f5e341
- Put unit cache container extract on new lines · 4175e3c0
  Gervaise Henry authored 4 years ago
  
  4175e3c0
- Update reference and version files · 695bc202
  Gervaise Henry authored 4 years ago
  
  695bc202
- Use cached images for unit tests · a3b6bade
  Gervaise Henry authored 4 years ago
  
  a3b6bade
- Put trackStart container in nextflow.config · c6a559e6
  Gervaise Henry authored 4 years ago
  
  c6a559e6
- Try to not error on version collect · 024e7e2c
  Gervaise Henry authored 4 years ago
  
  024e7e2c
- Temp remove seqwho version · 6aa080b2
  Gervaise Henry authored 4 years ago
  
  6aa080b2
- Sep images for version colleciton · e61faa4b
  Gervaise Henry authored 4 years ago
  
  e61faa4b
- Return echo to sif names · 3eab124a
  Gervaise Henry authored 4 years ago
  
  3eab124a
- Fix sif names · 59b4661c
  Gervaise Henry authored 4 years ago
  
  59b4661c
- Remove & from version collect · 4cbda573
  Gervaise Henry authored 4 years ago
  
  4cbda573
- Make entire version collect ci single set · d6280a4b
  Gervaise Henry authored 4 years ago
  
  d6280a4b
- Try echo sif before run · 637d98b5
  Gervaise Henry authored 4 years ago
  
  637d98b5
- Add quotes around img name · ff2f89f0
  Gervaise Henry authored 4 years ago
  
  ff2f89f0
- Put sif names together · 469ef281
  Gervaise Henry authored 4 years ago
  
  469ef281
- Temp echo sif · 27f3b44f
  Gervaise Henry authored 4 years ago
  
  27f3b44f
- Try to not error if images already there · a6b4db92
  Gervaise Henry authored 4 years ago
  
  a6b4db92
- Try to not error if images already there · c99049e9
  Gervaise Henry authored 4 years ago
  
  c99049e9
- Dynamically extract containers for cache and version extraction · 1d711568
  Gervaise Henry authored 4 years ago
  
  1d711568
- Parallelize cache singularity images · cc680428
  Gervaise Henry authored 4 years ago
  
  cc680428
- Display singularity cache · 0d01fd1c
  Gervaise Henry authored 4 years ago
  
  0d01fd1c
- Put version collection after cacheing · e697def7
  Gervaise Henry authored 4 years ago
  
  e697def7
- Fix ci lint · 49771d51
  Gervaise Henry authored 4 years ago
  
  49771d51
- Add singularity cache ci and collect version collections · 15162d84
  Gervaise Henry authored 4 years ago
  
  15162d84
- Add singularity cache to all nextflow runs · 4ada2322
  Gervaise Henry authored 4 years ago
  
  4ada2322
- Add singularity cache to start before script · 1383fb10
  Gervaise Henry authored 4 years ago
  
  1383fb10
- Add back singulity cache for each run · 0de01c80
  Gervaise Henry authored 4 years ago
  
  0de01c80
- Update configs · 5e5b14e1
  Gervaise Henry authored 4 years ago
  
  5e5b14e1
- Remove singularity cache clean · 6f1db39b
  Gervaise Henry authored 4 years ago
  
  6f1db39b
- temporarily clear singularity cache · 363b1b17
  Gervaise Henry authored 4 years ago
  
  363b1b17
- Add singularity cache to every singularity run command in ci · 5883960d
  Gervaise Henry authored 4 years ago
  
  5883960d
- Add singularity cache to before script in ci · 3cf19393
  Gervaise Henry authored 4 years ago
  
  3cf19393
- Add singularity cache to before script in ci · b53b14cf
  Gervaise Henry authored 4 years ago
  
  b53b14cf
- Update link from version report to wiki · e10247c7
  Gervaise Henry authored 4 years ago
  
  e10247c7
- Add new references to doc · ef3acdb0
  Gervaise Henry authored 4 years ago
  
  ef3acdb0
- Try to ignore err from seqtk version extraction · 43153b59
  Gervaise Henry authored 4 years ago
  
  43153b59
- Fix seqtk version extraction · 362879d3
  Gervaise Henry authored 4 years ago
  
  362879d3
- Try and fix seqtk version collection in unit test · 5a86b737
  Gervaise Henry authored 4 years ago
  
  5a86b737
- Remove unnecessary configs · 3bf03548
  Gervaise Henry authored 4 years ago
  
  3bf03548
- Fix downsample ci · fcab3193
  Gervaise Henry authored 4 years ago
  
  fcab3193
- Fix multiqc · 79adbc3a
  Gervaise Henry authored 4 years ago
  
  79adbc3a
- Fix tabing in multiqc config · 25a58702
  Gervaise Henry authored 4 years ago
  
  25a58702
- Add seqtk to references · 36caf093
  Gervaise Henry authored 4 years ago
  
  36caf093
- Fix extra tab in seqwho multiqc tsv · 2c70b0fc
  Gervaise Henry authored 4 years ago
  
  2c70b0fc
- Fix no download for fastqForce · aecc04e6
  Gervaise Henry authored 4 years ago
  
  aecc04e6
- Try to fix fastq count with fastq override · bbb54705
  Gervaise Henry authored 4 years ago
  
  bbb54705
- Fix endsForce test · 46772889
  Gervaise Henry authored 4 years ago
  
  46772889
- Fix ends force · bfe6bebc
  Gervaise Henry authored 4 years ago
  
  bfe6bebc
- Change getData fastqForce varible to param · 3026d63e
  Gervaise Henry authored 4 years ago
  
  3026d63e
- Set fastq count temporarily to zero if overridden · d633e19c
  Gervaise Henry authored 4 years ago
  
  d633e19c
- Fix seqwho tsv output for multiqc · 8f50b748
  Gervaise Henry authored 4 years ago
  
  8f50b748
- Add ends override · d3e19ff3
  Gervaise Henry authored 4 years ago
  
  d3e19ff3
- Don't donwload fastqs if overridden · 1e8d161e
  Gervaise Henry authored 4 years ago
  
  1e8d161e
- Update changelog · 30abfb69
  Gervaise Henry authored 4 years ago
  
  30abfb69
- Fix seqwho multiqc table · a9ee163f
  Gervaise Henry authored 4 years ago
  
  a9ee163f
- Add seqwho infer QC table to multiqc · d1271604
  Gervaise Henry authored 4 years ago
  
  d1271604
Mar 01, 2021
- Add missing speciesError to when · d9be943e
  Gervaise Henry authored 4 years ago
  
  d9be943e
- Put multiple when's into a single line · 84dd8e50
  Gervaise Henry authored 4 years ago
  
  84dd8e50
- Add handeling for low confidence seq type · 7a096fd5
  Gervaise Henry authored 4 years ago
  
  7a096fd5
Feb 28, 2021
- Disconnect confidence from species and seq type inference · b858a9d7
  Gervaise Henry authored 4 years ago
  
  b858a9d7
- Add quotes to seqwho error · 43f749d8
  Gervaise Henry authored 4 years ago
  
  43f749d8
- Add quotes to seqwho error · eec5b4c5
  Gervaise Henry authored 4 years ago
  
  eec5b4c5
- Merge dnanexus changes · edd49982
  Gervaise Henry authored 4 years ago
  
  edd49982
Feb 24, 2021
- Fix nf reference in ci · 94d3aaaa
  Gervaise Henry authored 4 years ago
  
  94d3aaaa
- Move nf and confs to match nextflow format · f8eeebc2
  Gervaise Henry authored 4 years ago
  
  f8eeebc2
Feb 23, 2021
- Add back mkdir -p in seqwho unit test · 6e2c01a8
  Gervaise Henry authored 4 years ago
  
  6e2c01a8
- Try removing ./ from seqwho -f in unit test · 91930b4a
  Gervaise Henry authored 4 years ago
  
  91930b4a
- Make dummy dir for plots · 6b2a74d6
  Gervaise Henry authored 4 years ago
  
  6b2a74d6
- Fix seqwho version collection in ci · 7b90b9dc
  Gervaise Henry authored 4 years ago
  
  7b90b9dc
- Use datahub as source for integration_se ci · 3ce1ddf7
  Gervaise Henry authored 4 years ago
  
  3ce1ddf7
- Fix ci lint · ba58c650
  Gervaise Henry authored 4 years ago
  
  ba58c650
- Replace species inference with seqwho · 634fd8a3
  Gervaise Henry authored 4 years ago
  
  634fd8a3
Feb 19, 2021
- Add test for seq type failure · 50715724
  Gervaise Henry authored 4 years ago
  
  50715724

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