fls-bioinformatics-core auto_process_ngs issues

fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.

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Read CSS and Javascript for QC reports from external files

#985 pjbriggs opened 7 hours ago
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Updates to QC report generation

#984 pjbriggs opened 23 hours ago
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Fix bug when truncating read lengths in bases mask with missing I5 index in sample sheet

#983 pjbriggs closed 2 days ago
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Update handling of metadata and QC protocols for 10x Genomics Visium data

#982 pjbriggs opened 2 days ago
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Refactor metadata and QC protocols for 10x Visium projects

#981 pjbriggs opened 3 days ago
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'publish_qc': fix QC verification for projects with custom protocols

#980 pjbriggs closed 2 days ago
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'publish_qc' command doesn't properly verify non-standard QC protocols

#979 pjbriggs closed 2 days ago
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Add support for RSeQC 'infer_experiment.py' as explicit QC module

#978 pjbriggs opened 1 week ago
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New QC protocol for 10x Genomics Visium HD spatial GEX data

#977 pjbriggs closed 2 days ago
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'run_qc.py': enable user to specify or customise QC protocols

#976 pjbriggs closed 5 hours ago
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auto-process-ngs version 0.41.0

#975 pjbriggs closed 1 week ago
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'make_fastqs': add sequence length statistics to processing QC

#974 pjbriggs closed 1 week ago
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'update' command: update stored project name when project is relocated

#973 pjbriggs closed 1 week ago
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'make_fastqs ': fix handling of read length truncation

#972 pjbriggs closed 1 week ago
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Remove 'fastq strand.py' ('strandedness' module) from QC protocols

#971 pjbriggs closed 1 week ago
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transfer_data.py: include analysis number in destination names

#970 pjbriggs closed 3 weeks ago
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transfer_data.py: enable filtering of Fastqs on sample name

#969 pjbriggs closed 3 weeks ago
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Fix handling alternative naming of RunParameters.xml file in 'setup' command

#968 pjbriggs closed 3 weeks ago
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auto-process-ngs version 0.40.0

#967 pjbriggs closed 4 weeks ago
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'run_qc.py': new command line options for Fastq verification and biological samples

#966 pjbriggs closed 1 month ago
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Update and refactor QC pipeline tests

#965 pjbriggs closed 3 weeks ago
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'make_fastqs': enable R1/R2 read truncation to be specified on command line

#964 pjbriggs closed 2 months ago
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auto-process-ngs version 0.39.0

#963 pjbriggs closed 2 months ago
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Update versions of QC dependencies: FastQC, FastqScreen & MultiQC

#962 pjbriggs closed 4 weeks ago
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Update Fastq generation for Spaceranger 3.0.0

#961 pjbriggs closed 2 months ago
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Fixes required for 'clone' command

#960 pjbriggs opened 2 months ago
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Update Fastq generation for compatibility with Spaceranger 3.0.0

#959 pjbriggs closed 2 months ago
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Explicitly store 'run ID' and 'run reference ID' in analysis directory metadata

#958 pjbriggs closed 4 weeks ago
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Explicitly store list of multiplexed samples in project metadata

#957 pjbriggs closed 2 months ago
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Update Fastq generation and QC pipelines for Cellranger 8.0.0

#956 pjbriggs closed 2 months ago
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Explicitly store number and names of multiplexed samples and use in reporting

#955 pjbriggs closed 2 months ago
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Add analysis version number to subdir name in 'transfer_data.py'

#954 pjbriggs closed 3 weeks ago
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auto-process-ngs version 0.38.0

#953 pjbriggs closed 3 months ago
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'make_fastqs': add specific protocol for Parse Evercode single cell data

#952 pjbriggs closed 3 months ago
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Add 'TCR scRNA-seq' and 'WT scRNA-seq' as recognised libraries for Parse Evercode

#951 pjbriggs closed 3 months ago
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Allow subsets of samples to be specified in 'transfer_data.py'

#950 pjbriggs closed 3 weeks ago
1
Update documentation for handling single cell and spatial data

#949 pjbriggs closed 4 months ago
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Enable 'pipeliner' tasks to be forced to run even if preceeding tasks have failed

#948 pjbriggs opened 4 months ago
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'report' command: fix reporting of samples for 10xGenomics Flex data

#947 pjbriggs closed 4 months ago
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Update versions for Fastqc, Fastq Screen & MultiQC in QC pipeline

#946 pjbriggs closed 4 weeks ago
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Fix CI tests when using 'pytest' version 8

#945 pjbriggs closed 5 months ago
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Unit tests broken for Python 3.8/pytest 8.0.0 in Github CI tests

#944 pjbriggs closed 5 months ago
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Split large unit test files into multiple smaller test files

#943 pjbriggs closed 5 months ago
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Optimise copying final data for some tasks in QC pipeline

#942 pjbriggs closed 5 months ago
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Add 10xGenomics Chromium 3' as a known 10x platform

#941 pjbriggs closed 5 months ago
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'archive' refuses to perform final archiving if empty 'Visium_images' dirs are present

#940 pjbriggs closed 5 months ago
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Enable QC reporting to include arbitrary externally generated outputs

#939 pjbriggs closed 5 months ago
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build(deps): bump readthedocs-sphinx-search from 0.3.1 to 0.3.2 in /docs

#938 dependabot[bot] closed 5 months ago
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qc/utils: update the conda dependencies in 'report_qc' function

#937 pjbriggs closed 5 months ago
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'make_fastqs': apply index filter options to Cellranger

#936 pjbriggs closed 5 months ago
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