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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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Enable '__repr__' method on QCProtocol class & recover instances from 'repr' string
#844
pjbriggs
closed
1 year ago
0
run_qc.py: add --info option to report protocols, organisms and reference data
#843
pjbriggs
closed
1 year ago
0
'run_qc' command: refactor how indexes are fetched from configuration
#842
pjbriggs
closed
1 year ago
0
'cellranger mkfastq' should get local cores and memory per core from execution environment
#841
pjbriggs
opened
1 year ago
0
Move code for the standalone 'run_qc.py' utility into CLI submodule
#840
pjbriggs
closed
1 year ago
0
Add flow cell mode for the parent run to the HTML QC reports
#839
pjbriggs
closed
1 year ago
0
Add flow cell information to metadata included in project QC reports
#838
pjbriggs
closed
1 year ago
1
applications: enable ssh/scp to handle empty remote user arguments
#837
pjbriggs
closed
1 year ago
0
auto-process-ngs version 0.33.0
#836
pjbriggs
closed
1 year ago
0
Standalone QC pipeline remove large temporary files on completion?
#835
pjbriggs
opened
1 year ago
0
Add 'read ranges' to QC protocols for 10x Flex data
#834
pjbriggs
closed
1 year ago
0
Remove the 'envmod' module from the library
#833
pjbriggs
closed
1 year ago
0
Fix bug setting 10x Genomics cell count from 'cellranger multi' in QC
#832
pjbriggs
closed
1 year ago
0
Update pipelines for CellRanger 7.1.0
#831
pjbriggs
closed
1 year ago
0
Add support for 10xGenomics fixed RNA profiling ("Flex")
#830
pjbriggs
closed
1 year ago
0
'setup' command: fix bug when supplied sample sheet is on a remote system
#829
pjbriggs
closed
1 year ago
0
Refactor 10x classes and utilities from 'tenx_genomics_utils' module
#828
pjbriggs
closed
1 year ago
0
Update the documentation for the 'setup' command
#827
pjbriggs
closed
1 year ago
0
'setup': allow facility run number to be set from command line
#826
pjbriggs
closed
1 year ago
0
Update 'add_command' decorator for 'AutoProcessor' class
#825
pjbriggs
closed
1 year ago
0
Extract file fetching code from 'setup' command into new function
#824
pjbriggs
closed
1 year ago
0
Relocate the 'Location' class from 'fileops' to 'utils' library module
#823
pjbriggs
closed
1 year ago
0
Escape spaces in 'source' and 'target' for 'rsync' commands
#822
pjbriggs
closed
1 year ago
0
Fix bug in QC verification when organism name contains spaces
#821
pjbriggs
closed
1 year ago
0
Fix bug in TSV with collated insert sizes in QC pipeline
#820
pjbriggs
closed
1 year ago
0
run_qc.py: allow STAR index to be specified explicitly
#819
pjbriggs
closed
1 year ago
0
'report' command: make major command line options mutually exclusive …
#818
pjbriggs
closed
1 year ago
0
New functionality for the 'samplesheet' command
#817
pjbriggs
closed
1 year ago
0
Update Github Python CI workflow to fix missing Python 3.6
#816
pjbriggs
closed
1 year ago
0
make_fastqs: capture NovaSeq flow cell mode
#815
pjbriggs
closed
1 year ago
0
Update QC for non-biological samples in 10xGenomics CellPlex datasets
#814
pjbriggs
closed
1 year ago
0
Fix locating linked samples in 10x Single Cell Multiome projects
#813
pjbriggs
closed
1 year ago
0
Updates to the 'publish_qc' command: suppress warnings, specify URL, fix reported destination etc
#812
pjbriggs
closed
1 year ago
0
QC pipeline: generate BED file for 'infer_experiment.py' from GTF annotation
#811
pjbriggs
closed
1 year ago
0
Update and fix Fastq read subsetting in 'run_qc'
#810
pjbriggs
closed
1 year ago
0
Update available job runners in configuration
#809
pjbriggs
closed
1 year ago
0
Remove duplicated content from the 'requirements' documentation
#808
pjbriggs
closed
1 year ago
0
Fix broken utility documentation generation
#807
pjbriggs
closed
1 year ago
0
QC pipeline: explicitly disable DISPLAY env variable in Qualimap task
#806
pjbriggs
closed
1 year ago
0
QC pipeline: fix handling of non-canonical Fastq names for grouping/BAM file generation
#805
pjbriggs
closed
1 year ago
0
run_qc.py: always generate HTML report
#804
pjbriggs
closed
1 year ago
0
Update QC pipeline to operate based on "QC modules" defined in protocols
#803
pjbriggs
closed
1 year ago
0
auto-process-ngs version 0.32.0
#802
pjbriggs
closed
1 year ago
0
auto-process-ngs version 0.31.0
#801
pjbriggs
closed
1 year ago
0
auto-process-ngs version 0.31.0.
#800
pjbriggs
closed
1 year ago
0
tenx_genomics_utils: fix broken version checking in the 'AtacSummary' class
#799
pjbriggs
closed
1 year ago
0
Fix reporting of sample names for 10x Genomics CellPlex datasets
#798
pjbriggs
closed
1 year ago
0
Skip single library analyses in QC for CellPlex data when config file is absent
#797
pjbriggs
closed
1 year ago
0
10x CellPlex: reported number of samples should be number of multiplexed samples
#796
pjbriggs
closed
1 year ago
0
10x CellPlex: QC shouldn't run single library analysis for multiplexing capture Fastqs
#795
pjbriggs
closed
1 year ago
0
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