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Created with Raphaël 2.2.010Aug43231Jul2813121129Jun2221178731May25242320191812104219Apr1312129Mar2325Feb2324Jan1314Dec13723Nov221918171615227Oct1486542130Sep29730Aug2623181321Jul1418Jun153May230Apr29723Mar15Feb8Dec27Oct30Sep28239328Aug27262524191730Jun10Feb69Jan826Nov2518Oct171625Sep23Refactored to use tuples for passing linked information through channels, parameterized some hard-coded valuesemma-cnvemma-cnvAlternative samplesheet for cnv calling - bam/bai files instead of fastq1/fastq2Tidied up some unneeded print statements and commentsRemoved package installation, chromosome prefix removal, fixed output directory trailing slashUpdated scripts location to bin sub-folder for Mike's prioritization scriptsMoved scripts into bin folderReducing CI memoryMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exomeSplitting variants by filter classification and adding fetal panel processingSplitting off cram compression into its own workflowAdd document describing running process of CNV-calling pipeline cnv calling pipeline running on eddieExomeDepth with nextflow runs with premade referencescreate references that can be loaded in rather than processed each timepass family variable into new processrun_exomedepth works, adding process to get proband cnvs that are not in parentsextract ids, sex and path from ped and samplesheet in cnv-callingsave progress on cnv_calling.nfMaking extract_*_FAM_PRO_ID.py Python 3, taking 1+ Ped files. Moving param defaults from main.nf to nextflow.config. Splitting Cram compression off into its own workflow. Making validation.nf less spammy. Adding channel documentaton. Adding pre-DECIPHER variant prioritisation. Making test family IDs reflect reality better.Add ExomeDepth to cnv_calling.nf, arguments set in commandresolve merge conflictsaving files that would be overwrittencommit all local filesfix merge issuecommit of local filesMerge branch 'emma-cnv' of https://git.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome into emma-cnvcommit functioning test pipeline commitUpdate run_on_eddie_guide.md Update run_on_eddie_guide.md Merge branch 'nextflow_config_fix' into 'master'Merge branch 'peddy-validation-to-bin' into 'master'Fixed peddy validation, sample id cleanup for underscore stripping, simplified sample preparation processesMerge branch 'master' into 'nextflow_config_fix'Update run_on_eddie_guide.md Begin creating eddie guideReducing CI memoryMerge branch 'mwham_develop' into 'master'Fixing bcbio template, removing test duplicateTrying custom Docker image, exiting properly from stub testsTrying Docker build