Quick pycode organization adjustments #94
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DarianHole
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Apr 30, 2024
* adjust config spacing, param location and resources, remove some unused params * initial cleanup * Remove illumina specific workflows and params * bump required nf version * remove bam-to-cram module, adjust resources * adjust how main handles input directory for both flat and barcoded inputs * initial pass to remove duplicate work, fix formatting, and improve flow * fix missed variable changes * fix other missed spots with tuples * fix to failing sample reporting * remove unneeded module, adjust guppyplex output * fix naming and empty file tracking for medaka * initial qc adjustments to match other medaka changes * Adding better function definitions to python functions (#94) * fix wrong brackets for barcode regex * rework scheme implementation * adjust ncov-tools to allow different prefixs * update help and config to match * adjust git ci test scripts * remove previous test files that are not run * add a second sample for tests * remove additional ci test files, unneeded * fix schemes * adjust schemes validation * make aligned file optional * adjust metadata input for ncov-tools fixing missing file * small test adjustment * fix up scheme input validation * add in initial nextclade implementation * fix up process tracking * add version tracking to where it was missing * adjust module formatting * consistent module variable formatting * removal of duplicate checks, fix upload of fast5s * fix nml config, add in nc results correction to qc * adjust qc script for fs flags * remove nextflow_qc_pass column and adjust the tracking * Switch to all snake_case params. Add readme updates and changelog * add medaka model to version tracking * final adjustments with schemes and steps * add a bit more info to the changelog
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Adding better function definitions to the written python code to make it more readable