Issues

• MD5s for automated processing re-run do not match

  bugquestionsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#83 · Filter by author erflynn opened on Jul 15, 2024
  10

  

• single-cell additional info parsing

  UCSF-DSCOLAB/data_processing_pipelines#80 · Filter by author dtm2451 opened on Jun 26, 2024

• single-cell umap file name ambiguity

  UCSF-DSCOLAB/data_processing_pipelines#79 · Filter by author dtm2451 opened on Jun 26, 2024

• Clean up of workflow, add tests for new functions

  enhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#77 · Filter by author erflynn opened on May 23, 2024

• Testing snapshot stdout

  bugsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#76 · Filter by author erflynn opened on May 23, 2024

• sc-seq diagnostic plot improvements

  bugenhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#75 · Filter by author erflynn opened on May 20, 2024

• Depooling pipeline does not leverage slurm

  bug
  UCSF-DSCOLAB/data_processing_pipelines#73 · Filter by author amadeovezz opened on Apr 18, 2024
  1

  

• sc_seq pipeline diagnostic plots for nCount_ADT are unusable

  UCSF-DSCOLAB/data_processing_pipelines#72 · Filter by author dtm2451 opened on Mar 26, 2024

• sc_seq pipeline should pull in or organize more TCR/BCR info

  UCSF-DSCOLAB/data_processing_pipelines#68 · Filter by author dtm2451 opened on Mar 11, 2024
  

• Tests are not localized

  bugsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#64 · Filter by author amadeovezz opened on Dec 7, 2023

• pull in amazing cluster dispersion QC plots

  enhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#61 · Filter by author erflynn opened on Dec 2, 2023
  1

• Simplify user configuration for reference genomes for bulk RNAseq

  bulkenhancement
  UCSF-DSCOLAB/data_processing_pipelines#58 · Filter by author AlaaALatif opened on Nov 17, 2023

• Trace bug while running tests

  bugsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#57 · Filter by author amadeovezz opened on Nov 13, 2023

• Single-cell tests have harcoded paths

  bugsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#55 · Filter by author amadeovezz opened on Nov 9, 2023
  

• post-merge filtering of variants in bulk pipeline

  bulkenhancement
  UCSF-DSCOLAB/data_processing_pipelines#52 · Filter by author erflynn opened on Nov 6, 2023
  1

• Re-start after Dsc-pileup or merge

  enhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#51 · Filter by author erflynn opened on Nov 3, 2023

• Get nextflow to submit to specified partition

  UCSF-DSCOLAB/data_processing_pipelines#50 · Filter by author erflynn opened on Nov 3, 2023
  1

• Seperate out Freemuxlet and Demuxlet into two composable pipelines

  enhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#49 · Filter by author amadeovezz opened on Nov 2, 2023
  

• Improve test cases for single cell

  enhancementsingle-celltesting
  UCSF-DSCOLAB/data_processing_pipelines#48 · Filter by author amadeovezz opened on Nov 2, 2023
  2

  

• fix run_resume.sh script

  bugsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#47 · Filter by author erflynn opened on Nov 2, 2023

• Update pre-fmx-qc option to match pre-qc

  bugsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#45 · Filter by author erflynn opened on Nov 1, 2023

• Check if we can set a limit to resources consumed by nextflow

  enhancementquestion
  UCSF-DSCOLAB/data_processing_pipelines#43 · Filter by author amadeovezz opened on Oct 31, 2023
  1

  

• Deletes working during if OOT error

  bugsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#41 · Filter by author erflynn opened on Oct 30, 2023
  1

• Make outputs sync with metis model for bulk

  bulkenhancement
  UCSF-DSCOLAB/data_processing_pipelines#39 · Filter by author erflynn opened on Oct 27, 2023
  1

  

• De-pool piepline for fully demultiplexed scRNAseq data

  enhancementsingle-cell
  UCSF-DSCOLAB/data_processing_pipelines#37 · Filter by author dtm2451 opened on Oct 23, 2023
  2