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Created with Raphaël 2.2.029Aug221817161523Jun2216141312922May121014Apr31Mar291510Feb8Dec12Oct15Sep24Aug16151043231Jul2813121129Jun2221178731May25242320191812104219Apr1312129Mar2325Feb2324Jan1314Dec13723Nov221918171615227Oct1486542130Sep29730Aug2623181321Jul1418Jun153May230Apr29723Mar15Feb8Dec27Oct30Sep28239328Aug27262524191730Jun10Feb69Jan826Nov2518Oct171625Sep23Added VEP effects to configChanged sort order of families by batch instead of date, added steps for setting parent field to 0 for shared-affected families, description of step for DECIPHER upload file copyFixed position of defining SHORT_PROJECT_ID variableRemoving null_if_stubs, fixing write_bcbio_csv, applying changes from c7dff4e8, making run_stubs.sh delete less stuffFixed commented out sectionRe-analysis preparation SOP, scripts, and assets - tested on 20230816_reanalysisFixing argparse in extract_solo_FAM_PRO_ID.py, adding exit statements to IGV in NF script, cleaning up IGV singularity imageUpdated G2P panelInitial commit of SOP for preparation for annual re-analysisMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into mwham_developRead individual ids from params dir ped fileAllow for suffixes in family namesPull QC metrics for reportHelper script for fixing ids in output family infoUpdated scripts to handle IGV automated snapshot generationTemplate updateIGV automatic snapshot generationFixing split_trio_solo_variants.pyAdding png splitting stage and NHS output dirFixing IGV/xvfb/Singularity. Using absolute paths in snapshot files. Adding bam indexes to channelsDisentangling spaghetti. Removing old prioritisation process, merging prioritisation and setup, using watchPath/fromPath to pick up or wait for decipher file. Adding igv stub. Adding fake test asset filesMerge branch 'variant_prioritisation' into 'master'Merge branch 'master' into 'variant_prioritisation'Added GATK Haplotype new parameters on active probability threshold and interval paddingFixing stub testsFixing dnu_cleanAdding strand bias correction from process_trio.shMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into variant_prioritisationAdding programs.txt, fixing some prioritisation output locationsFS/SOR filtering/flagging for fetal anomaliesFixing g2p and decipher file generationFixing decipher scripts for Nextflow, adding genome reference dict and VEP params, fixing Conda. Splitting denovo VCF filtering from VASESegmenting variant prioritisation, adding stub tests. Making Conda optional when running stubs. Making prioritisation scripts executable, compatible with Nextflow channels.Merge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exomeUpdated prioritization scripts to include FS/SOR flag filteringScripts for computing DDD coverage statsFixing prioritisation outputs, adding bam index, making prioritisation console output less spammyVar prioritisation/cram compression fixes. Fixing BCBio output collation. Adding var prioritisation GiaB testFixed peddy validation script paramsUpdated processing scripts