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76 Open 233 Closed
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Issues list

Bug with missing 'end_time' when auditing pipeline compute bug pipeliner
#1027 opened Feb 21, 2025 by pjbriggs
'make_fastqs': force splitting of lanes when sample names are duplicated in different projects bug Fastq generation
#1024 opened Feb 19, 2025 by pjbriggs
transfer_data.py: add option to include images for 10x Visium datasets 10xGenomics Data transfer new functionality
#1023 opened Feb 17, 2025 by pjbriggs
'transfer_data.py': include .cloupe files from Cellranger 10xGenomics Data transfer enhancement
#1022 opened Feb 17, 2025 by pjbriggs
'transfer_data.py': tarring 10x outputs gives errors ("File removed before we read it") 10xGenomics bug Data transfer
#1021 opened Feb 17, 2025 by pjbriggs
Update Github runner image from deprecated 'ubuntu-20.04' and drop support for Python 3.6 in CI tests testing update
#1020 opened Feb 13, 2025 by pjbriggs
RSeQC genebody_coverage.py ZeroDivisionError failures in QC pipeline bug QC pipeline
#1017 opened Feb 13, 2025 by pjbriggs
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
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
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