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Issues list

Update Fastq generation protocol for 10x Genomics single cell data for Cellranger 9+ 10xGenomics Fastq generation update
#1013 opened Dec 17, 2024 by pjbriggs
Add support for 10x 5’ immune profiling libraries pooled with hashtags to QC pipeline 10xGenomics new functionality QC pipeline QC reporting
#1012 opened Dec 17, 2024 by pjbriggs
Add support for Cellranger 9.0.0 in pipelines 10xGenomics Fastq generation QC pipeline QC reporting update
#1010 opened Dec 9, 2024 by pjbriggs
Change name of 'README.info' metdata files in analysis project directories enhancement metadata
#1004 opened Oct 30, 2024 by pjbriggs
Add explicit IDs to sample sets within a run enhancement metadata
#1003 opened Oct 30, 2024 by pjbriggs
Enable use of custom adapter file for FastQC in QC pipeline new functionality qc metrics QC pipeline QC reporting
#992 opened Jul 31, 2024 by pjbriggs
Report poly-G content as part of QC pipeline new functionality qc metrics QC pipeline QC reporting
#991 opened Jul 31, 2024 by pjbriggs
Options to update archived run after 'final' archiving operation Archiving new functionality
#989 opened Jul 17, 2024 by pjbriggs
Fixes required for 'clone' command bug Cloning enhancement
#960 opened Apr 16, 2024 by pjbriggs
config: allow aliases to be defined for organisms configuration enhancement QC pipeline
#935 opened Jan 11, 2024 by pjbriggs
Fastq generation and QC: add option to inject local setup script into job scripts Fastq generation new feature pipeliner QC pipeline
#933 opened Jan 10, 2024 by pjbriggs
'make_fastqs': put processing outputs and stats into a single 'processing' subdirectory Fastq generation new feature
#932 opened Jan 10, 2024 by pjbriggs
Include processing details in QC reports Fastq generation new feature Reporting
#928 opened Dec 20, 2023 by pjbriggs
Consolidate updating metadata and paths across archive and update commands Archiving metadata refactoring
#909 opened Nov 1, 2023 by pjbriggs
Remove 'update_project_metadata.py' utility and put useful functionality into 'update' command enhancement metadata refactoring
#898 opened Oct 24, 2023 by pjbriggs
Add documentation for the 'update' command documentation enhancement metadata
#897 opened Oct 24, 2023 by pjbriggs
Retire code for processing ICELL8 single cell data? ICELL8 refactoring
#892 opened Oct 20, 2023 by pjbriggs
'make_fastqs': strip trailing Ns from index sequences in sample sheets enhancement Fastq generation
#875 opened Jul 24, 2023 by pjbriggs
Enable Fastq generation to separate projects within lane subsets Fastq generation new feature
#855 opened May 2, 2023 by pjbriggs
'cellranger mkfastq' should get local cores and memory per core from execution environment 10xGenomics bug Fastq generation
#841 opened Mar 29, 2023 by pjbriggs
Standalone QC pipeline remove large temporary files on completion? enhancement QC pipeline Standalone QC
#835 opened Feb 21, 2023 by pjbriggs
Refactor batching of commands in Pipeliner pipeliner refactoring
#776 opened May 12, 2022 by pjbriggs
Handle legacy metadata items (e.g. assay) enhancement metadata papercut
#769 opened Mar 18, 2022 by pjbriggs
Extend PipelineTasks to facilitate creating directories and moving/copying files new feature pipeliner
#759 opened Feb 18, 2022 by pjbriggs
Add support for Python 3.9 and 3.10 python3 testing update
#758 opened Feb 16, 2022 by pjbriggs
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