Commits · emma-cnv · igmmbioinformatics / trio-whole-exome

Aug 10, 2022
- Refactored to use tuples for passing linked information through channels,... · 02ad391c
  user name authored 2 years ago
  
  Refactored to use tuples for passing linked information through channels, parameterized some hard-coded values
  02ad391c
- Alternative samplesheet for cnv calling - bam/bai files instead of fastq1/fastq2 · 462bb713
  user name authored 2 years ago
  
  462bb713
- Tidied up some unneeded print statements and comments · fcb7bd6f
  user name authored 2 years ago
  
  fcb7bd6f
- Removed package installation, chromosome prefix removal, fixed output directory trailing slash · b44265e7
  user name authored 2 years ago
  
  b44265e7
Jul 31, 2022
- Add document describing running process of CNV-calling pipeline · eb8a1fb3
  s1734289 authored 2 years ago
  
  eb8a1fb3
Jul 28, 2022
- cnv calling pipeline running on eddie · a38bdb8d
  3mma-mack authored 2 years ago
  
  a38bdb8d
Jul 13, 2022
- ExomeDepth with nextflow runs with premade references · 5679b28e
  3mma-mack authored 2 years ago
  
  5679b28e
- create references that can be loaded in rather than processed each time · babc1fd7
  3mma-mack authored 2 years ago
  
  babc1fd7
Jul 12, 2022
- pass family variable into new process · 163426c2
  3mma-mack authored 2 years ago
  
  163426c2
- run_exomedepth works, adding process to get proband cnvs that are not in parents · 64d340c7
  3mma-mack authored 2 years ago
  
  64d340c7
- extract ids, sex and path from ped and samplesheet in cnv-calling · 84564592
  3mma-mack authored 2 years ago
  
  84564592
- save progress on cnv_calling.nf · dff6b661
  3mma-mack authored 2 years ago
  
  dff6b661
Jul 11, 2022
- Add ExomeDepth to cnv_calling.nf, arguments set in command · c78b8199
  3mma-mack authored 2 years ago
  
  c78b8199
- resolve merge conflict · e4928e64
  3mma-mack authored 2 years ago
  
  e4928e64
- saving files that would be overwritten · 9564335e
  3mma-mack authored 2 years ago
  
  9564335e
- commit all local files · a94f342c
  3mma-mack authored 2 years ago
  
  a94f342c
- fix merge issue · 43810af8
  3mma-mack authored 2 years ago
  
  43810af8
- commit of local files · 6a2eef8a
  3mma-mack authored 2 years ago
  
  6a2eef8a
- Merge branch 'emma-cnv' of... · 2f64556b
  3mma-mack authored 2 years ago
  
  Merge branch 'emma-cnv' of https://git.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome into emma-cnv
  2f64556b
- commit functioning test pipeline commit · fca1deaf
  3mma-mack authored 2 years ago
  
  fca1deaf
Jun 29, 2022
- Update run_on_eddie_guide.md · 24ae182e
  s1734289 authored 2 years ago
  
  24ae182e
Jun 22, 2022
- Update run_on_eddie_guide.md · 8ad43113
  s1734289 authored 2 years ago
  
  8ad43113
- Merge branch 'nextflow_config_fix' into 'master' · 93b2f9a7
  mwham authored 2 years ago
  
  nextflow.config fix, move executor out of processes See merge request !6
  93b2f9a7
- Merge branch 'peddy-validation-to-bin' into 'master' · 1b7664b0
  mwham authored 2 years ago
  
  Fixed peddy validation, sample id cleanup for underscore stripping, simplified sample preparation processes See merge request !9
  1b7664b0
- Fixed peddy validation, sample id cleanup for underscore stripping, simplified... · 467982ca
  ameyner2 authored 2 years ago and mwham committed 2 years ago
  
  Fixed peddy validation, sample id cleanup for underscore stripping, simplified sample preparation processes
  467982ca
- Merge branch 'master' into 'nextflow_config_fix' · ef6b7662
  ameyner2 authored 2 years ago
  
  # Conflicts: # nextflow.config
  ef6b7662
- Update run_on_eddie_guide.md · bd20f643
  s1734289 authored 2 years ago
  
  bd20f643
- Begin creating eddie guide · 980905c7
  s1734289 authored 2 years ago
  
  980905c7
Jun 21, 2022
- Reducing CI memory · eddf83bc
  mwham authored 2 years ago
  
  eddf83bc
- Merge branch 'mwham_develop' into 'master' · b45bb079
  mwham authored 2 years ago
  
  Bin dir, CI build fixes See merge request !8
  b45bb079
Jun 17, 2022
- Fixing bcbio template, removing test duplicate · 4dc87258
  mwham authored 2 years ago
  
  4dc87258
Jun 08, 2022
- Trying custom Docker image, exiting properly from stub tests · 8a631e71
  mwham authored 2 years ago
  
  8a631e71
Jun 07, 2022
- Trying Docker build · 3def137e
  mwham authored 2 years ago
  
  3def137e
May 31, 2022
- Update Emma_daily_updates.md · c27a62df
  s1734289 authored 2 years ago
  
  c27a62df
May 25, 2022
- Add new file · 4486d42a
  s1734289 authored 2 years ago
  
  4486d42a
May 24, 2022
- Making min/max resources configurable, adding test stubs · acd6068e
  mwham authored 2 years ago
  
  acd6068e
- Update steps_to_run_tests_on_eddie.md · d4ad187a
  s1734289 authored 2 years ago
  
  d4ad187a
- Update steps_to_run_tests_on_eddie.md · cebb3d05
  s1734289 authored 2 years ago
  
  cebb3d05
- Update steps_to_run_tests_on_eddie.md · ba9acd36
  s1734289 authored 2 years ago
  
  ba9acd36
- Merge branch 'peddy-validation-to-bin' into mwham_develop · abf8d102
  mwham authored 2 years ago
  
  abf8d102