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fls-bioinformatics-core
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auto_process_ngs
Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Options to update archived run after 'final' archiving operation
#989
pjbriggs
opened
3 days ago
0
Add expected outputs from protocol to QC reporting
#988
pjbriggs
opened
1 week ago
0
auto-process-ngs version 0.42.0
#987
pjbriggs
closed
1 week ago
0
bcl2fastq/reporting: fix the barplot for masked/padded reads per Fastq.
#986
pjbriggs
closed
1 week ago
0
Read CSS and Javascript for QC reports from external files
#985
pjbriggs
opened
2 weeks ago
0
Updates to QC report generation
#984
pjbriggs
closed
1 week ago
0
Fix bug when truncating read lengths in bases mask with missing I5 index in sample sheet
#983
pjbriggs
closed
2 weeks ago
0
Update handling of metadata and QC protocols for 10x Genomics Visium data
#982
pjbriggs
closed
1 week ago
0
Refactor metadata and QC protocols for 10x Visium projects
#981
pjbriggs
closed
1 week ago
0
'publish_qc': fix QC verification for projects with custom protocols
#980
pjbriggs
closed
2 weeks ago
0
'publish_qc' command doesn't properly verify non-standard QC protocols
#979
pjbriggs
closed
2 weeks ago
0
Add support for RSeQC 'infer_experiment.py' as explicit QC module
#978
pjbriggs
closed
1 week ago
0
New QC protocol for 10x Genomics Visium HD spatial GEX data
#977
pjbriggs
closed
2 weeks ago
0
'run_qc.py': enable user to specify or customise QC protocols
#976
pjbriggs
closed
2 weeks ago
0
auto-process-ngs version 0.41.0
#975
pjbriggs
closed
3 weeks ago
0
'make_fastqs': add sequence length statistics to processing QC
#974
pjbriggs
closed
3 weeks ago
0
'update' command: update stored project name when project is relocated
#973
pjbriggs
closed
3 weeks ago
0
'make_fastqs ': fix handling of read length truncation
#972
pjbriggs
closed
3 weeks ago
0
Remove 'fastq strand.py' ('strandedness' module) from QC protocols
#971
pjbriggs
closed
3 weeks ago
0
transfer_data.py: include analysis number in destination names
#970
pjbriggs
closed
1 month ago
0
transfer_data.py: enable filtering of Fastqs on sample name
#969
pjbriggs
closed
1 month ago
0
Fix handling alternative naming of RunParameters.xml file in 'setup' command
#968
pjbriggs
closed
1 month ago
0
auto-process-ngs version 0.40.0
#967
pjbriggs
closed
1 month ago
0
'run_qc.py': new command line options for Fastq verification and biological samples
#966
pjbriggs
closed
1 month ago
0
Update and refactor QC pipeline tests
#965
pjbriggs
closed
1 month ago
0
'make_fastqs': enable R1/R2 read truncation to be specified on command line
#964
pjbriggs
closed
2 months ago
0
auto-process-ngs version 0.39.0
#963
pjbriggs
closed
2 months ago
0
Update versions of QC dependencies: FastQC, FastqScreen & MultiQC
#962
pjbriggs
closed
1 month ago
0
Update Fastq generation for Spaceranger 3.0.0
#961
pjbriggs
closed
2 months ago
0
Fixes required for 'clone' command
#960
pjbriggs
opened
3 months ago
0
Update Fastq generation for compatibility with Spaceranger 3.0.0
#959
pjbriggs
closed
2 months ago
0
Explicitly store 'run ID' and 'run reference ID' in analysis directory metadata
#958
pjbriggs
closed
1 month ago
0
Explicitly store list of multiplexed samples in project metadata
#957
pjbriggs
closed
3 months ago
0
Update Fastq generation and QC pipelines for Cellranger 8.0.0
#956
pjbriggs
closed
2 months ago
0
Explicitly store number and names of multiplexed samples and use in reporting
#955
pjbriggs
closed
3 months ago
0
Add analysis version number to subdir name in 'transfer_data.py'
#954
pjbriggs
closed
1 month ago
0
auto-process-ngs version 0.38.0
#953
pjbriggs
closed
3 months ago
0
'make_fastqs': add specific protocol for Parse Evercode single cell data
#952
pjbriggs
closed
3 months ago
0
Add 'TCR scRNA-seq' and 'WT scRNA-seq' as recognised libraries for Parse Evercode
#951
pjbriggs
closed
3 months ago
0
Allow subsets of samples to be specified in 'transfer_data.py'
#950
pjbriggs
closed
1 month ago
1
Update documentation for handling single cell and spatial data
#949
pjbriggs
closed
4 months ago
0
Enable 'pipeliner' tasks to be forced to run even if preceeding tasks have failed
#948
pjbriggs
opened
5 months ago
0
'report' command: fix reporting of samples for 10xGenomics Flex data
#947
pjbriggs
closed
5 months ago
0
Update versions for Fastqc, Fastq Screen & MultiQC in QC pipeline
#946
pjbriggs
closed
1 month ago
0
Fix CI tests when using 'pytest' version 8
#945
pjbriggs
closed
5 months ago
0
Unit tests broken for Python 3.8/pytest 8.0.0 in Github CI tests
#944
pjbriggs
closed
5 months ago
0
Split large unit test files into multiple smaller test files
#943
pjbriggs
closed
5 months ago
0
Optimise copying final data for some tasks in QC pipeline
#942
pjbriggs
closed
5 months ago
0
Add 10xGenomics Chromium 3' as a known 10x platform
#941
pjbriggs
closed
5 months ago
0
'archive' refuses to perform final archiving if empty 'Visium_images' dirs are present
#940
pjbriggs
closed
6 months ago
0
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