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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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auto-process-ngs version 0.35.0
#889
pjbriggs
closed
9 months ago
0
Update to work with Spaceranger 2.1.1
#888
pjbriggs
closed
9 months ago
0
'make_fastqs': add support to specify workflow for '10x_visium' protocol (Spaceranger --rc-i2-override)
#887
pjbriggs
closed
9 months ago
0
Explicitly disable adapter trimming when generating Fastqs for 10x Genomics Visium data
#886
pjbriggs
closed
9 months ago
1
Split large unit test files into multiple files
#885
pjbriggs
closed
5 months ago
1
Add options to trim reads in Fastq generation step
#884
pjbriggs
closed
2 months ago
0
Keep checksum file separate from ZIP archives when transferring Fastqs
#883
pjbriggs
closed
9 months ago
0
Data transfer: keep checksum file separate when making ZIP archives
#882
pjbriggs
closed
9 months ago
0
Refactor handling of auto_process configuration
#881
pjbriggs
closed
9 months ago
0
Enable job runner to be specified on command line for 'archive' command
#880
pjbriggs
closed
11 months ago
0
'publish_qc': don't delete/overwrite existing non-publication directory
#879
pjbriggs
closed
9 months ago
0
'publish_qc': add checks on deletion of existing content
#878
pjbriggs
closed
9 months ago
0
Move the MultiQC report generation into a separate task in the QC pipeline
#877
pjbriggs
opened
11 months ago
0
Update QC reporting to handle "external" 'cellranger multi' outputs
#876
pjbriggs
closed
9 months ago
0
'make_fastqs': strip trailing Ns from index sequences in sample sheets
#875
pjbriggs
opened
12 months ago
0
analyse_barcodes.py: prevent multiple counting of barcodes when Fastqs supplied on command line
#874
pjbriggs
closed
9 months ago
0
Verify integrity of Fastqs in QC pipeline
#873
pjbriggs
closed
8 months ago
0
Check hard links are possible when requested for transferring data
#872
pjbriggs
closed
9 months ago
0
transfer_data.py: add options to put Fastqs into ZIP files or exclude Fastqs
#871
pjbriggs
closed
9 months ago
0
transfer_data.py: add option to put Fastqs into a ZIP file for transfer
#870
pjbriggs
closed
9 months ago
0
Add functionality to generate concise summary of sample sheet outputs
#869
pjbriggs
closed
1 month ago
0
'setup': collect default bases mask and flow cell mode
#868
pjbriggs
closed
1 year ago
0
manage_fastqs.py: enable Fastqs to be batched into multiple ZIP files
#867
pjbriggs
closed
1 year ago
0
Allow biological data samples to be explicitly defined for QC pipeline
#866
pjbriggs
closed
12 months ago
0
Fix QC pipeline to correctly handle single-ended SRA Fastq data
#865
pjbriggs
closed
1 year ago
0
'transfer_data.py': ensure copied files have read-write permissions
#864
pjbriggs
closed
1 year ago
0
Add basic support for 10xGenomics single cell immune profiling data
#863
pjbriggs
closed
9 months ago
0
auto-process-ngs version 0.34.0
#862
pjbriggs
closed
1 year ago
0
analysis: update 'match_run_id' to account for analysis numbers
#861
pjbriggs
closed
1 year ago
0
'publish_qc' command: include README content in index
#860
pjbriggs
closed
1 year ago
0
Add 'analysis number' to analysis directory metadata and use for run ID
#859
pjbriggs
closed
1 year ago
0
Add dedicated runner for Picard tools in the QC pipeline
#858
pjbriggs
closed
1 year ago
0
Handle reporting 10xGenomics multiplexing metrics with multiple libraries
#857
pjbriggs
closed
1 year ago
0
Update the 10x_multi_config.csv template from 'setup_analysis_dirs'
#856
pjbriggs
closed
1 year ago
0
Enable Fastq generation to separate projects within lane subsets
#855
pjbriggs
opened
1 year ago
0
Add integrity check on gzipped Fastqs in QC pipeline
#854
pjbriggs
closed
8 months ago
1
Refactor handling of QC protocols within pipeline
#853
pjbriggs
closed
1 year ago
0
Implement run reference ID distinct from run ID
#852
pjbriggs
closed
1 year ago
0
Fix attribute extraction from sequence length files for non-canonical Fastq names
#851
pjbriggs
closed
1 year ago
0
Implement '10x_Visium_FFPE' QC protocol
#850
pjbriggs
closed
1 year ago
0
Implement option in 'transfer_fastqs.py' to copy subsets of Fastqs
#849
pjbriggs
closed
1 year ago
0
Update 'determine_qc_protocol' for Parse Evercode snRNA-seq
#848
pjbriggs
closed
1 year ago
0
Auto-generate table of QC protocols in 'run_qc' documentation
#847
pjbriggs
closed
1 year ago
0
Refactor 'reportqc.py' to move code into 'cli' submodule
#846
pjbriggs
closed
1 year ago
0
Add documentation on '--info' option of 'run_qc.py'
#845
pjbriggs
closed
1 year ago
0
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
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