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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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qc/utils: update the conda dependencies in 'report_qc' function
#937
pjbriggs
closed
5 months ago
0
'make_fastqs': apply index filter options to Cellranger
#936
pjbriggs
closed
5 months ago
0
config: allow aliases to be defined for organisms
#935
pjbriggs
opened
5 months ago
0
Add support for 10x Genomics Chromium 5' Single Cell Immune Profiling
#934
pjbriggs
closed
4 months ago
0
Fastq generation and QC: add option to inject local setup script into job scripts
#933
pjbriggs
opened
6 months ago
0
'make_fastqs': put processing outputs and stats into a single 'processing' subdirectory
#932
pjbriggs
opened
6 months ago
0
'archive' command should explicitly store the run ID and run reference
#931
pjbriggs
closed
1 month ago
0
auto-process-ngs version 0.37.0
#930
pjbriggs
closed
6 months ago
0
Fix broken unit test for 'setup' command for NovaSeq data
#929
pjbriggs
closed
6 months ago
0
Include processing details in QC reports
#928
pjbriggs
opened
6 months ago
0
Fix bug with splitting Fastqs by lane when QC pipeline is re-run
#927
pjbriggs
closed
6 months ago
0
'setup' command: force specification of the facility run number
#926
pjbriggs
closed
6 months ago
0
Fix bug in QC pipeline if working dir is on different device to QC dir
#925
pjbriggs
closed
6 months ago
0
run_qc.py should refuse to split Fastqs by lane for non-canonical names
#924
pjbriggs
closed
6 months ago
0
run_qc.py: fix incorrect default for --split-fastqs-by-lane
#923
pjbriggs
closed
6 months ago
0
Update QC protocols for 10x Visium spatial GEX and PEX data
#922
pjbriggs
closed
6 months ago
0
Update the list of platforms and applications in 'projects.info' documentation
#921
pjbriggs
closed
7 months ago
0
Update package versions required for building documentation
#920
pjbriggs
closed
7 months ago
0
Update documentation to add the ReadTheDocs theme
#919
pjbriggs
closed
7 months ago
0
auto-process-ngs version 0.36.0
#918
pjbriggs
closed
7 months ago
0
Check for invalid probe barcodes in '10x_multi_config.csv' files
#917
pjbriggs
opened
7 months ago
1
Implement functionality for per-lane QC in QC pipeline
#916
pjbriggs
closed
7 months ago
0
Fix documentation build failure on ReadTheDocs
#915
pjbriggs
closed
7 months ago
0
Fix bug when creating Fastqs in mock analysis projects without specifying lanes
#914
pjbriggs
closed
7 months ago
0
Separate undetermined reads by lane in Fastq generation step
#913
pjbriggs
closed
7 months ago
1
'update' command should also update project names
#912
pjbriggs
closed
2 weeks ago
0
Automatically assign project-specific log directories to tasks in the QC pipeline
#911
pjbriggs
closed
7 months ago
0
Set log directory for Cellranger acquisition task in QC pipeline
#910
pjbriggs
closed
8 months ago
0
Consolidate updating metadata and paths across `archive` and `update` commands
#909
pjbriggs
opened
8 months ago
0
Fix reporting path to analysis directory in 'report' command
#908
pjbriggs
closed
8 months ago
0
Fix updating stored paths when creating final archive
#907
pjbriggs
closed
8 months ago
0
Force specification of run number for the 'setup' command
#906
pjbriggs
closed
6 months ago
1
QC pipeline: only run GTF to BED conversion if output doesn't already exist.
#905
pjbriggs
closed
8 months ago
0
Explicitly specify 'numpy' version in conda dependencies for reporting in QC pipeline
#904
pjbriggs
closed
8 months ago
0
Reimplement conda dependency resolution as separate jobs in 'pipeliner' module
#903
pjbriggs
closed
7 months ago
0
Check if 'Visium_images' subdirectory is empty when archiving
#902
pjbriggs
closed
5 months ago
0
QC pipeline: only execute GTF to BED conversion if output file doesn't exist
#901
pjbriggs
closed
8 months ago
0
'auto_processor': update docstring for 'AutoProcess.load_project_metadata'
#900
pjbriggs
closed
8 months ago
0
'commands/make_fastq_cmd': drop unused import of 'time' module
#899
pjbriggs
closed
8 months ago
0
Remove 'update_project_metadata.py' utility and put useful functionality into 'update' command
#898
pjbriggs
opened
8 months ago
0
Add documentation for the 'update' command
#897
pjbriggs
opened
8 months ago
0
WIP new 'update' command to update and synchronise project metadata
#896
pjbriggs
closed
8 months ago
0
Implement new auto-process 'info' command
#895
pjbriggs
closed
6 months ago
0
Update documentation for handling 10x Genomics data
#894
pjbriggs
closed
7 months ago
0
Implement functionality to update & synchronise run and project metadata and paths
#893
pjbriggs
closed
8 months ago
0
Retire code for processing ICELL8 single cell data?
#892
pjbriggs
opened
8 months ago
0
Add support for 10x Genomics CytAssist Visium spatial RNA-seq platform
#891
pjbriggs
closed
8 months ago
0
Drop 'fastq_strand.py' in favour of RSeQC's 'infer_experiment.py' for strandedness
#890
pjbriggs
closed
2 weeks ago
0
auto-process-ngs version 0.35.0
#889
pjbriggs
closed
8 months ago
0
Update to work with Spaceranger 2.1.1
#888
pjbriggs
closed
8 months ago
0
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