Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
This PR enables the ability to analyze MPXV genomes with the intent to be able to easily add other viral pathogens in the future, like HIV, WNV, etc.
Separates stats_n_coverage into a new task in a quality_control folder
Moves consensus_qc into a new task in the quality_control folder
changes GENOME_LEN to be calculated from the reference genome if one is provided; the default is SC2 length. This will allow for proper calculation of percent_genome_coverage metrics
Moves fastq_scan tasks into quality_control folder
Moves fastqc tasks into quality_control folder
Deletes the qc_utils task file
Moves the SC2 gene coverage calculations into a SC2 specific task, task_sc2_genome_coverage.wdl
renames these output variables to be prefaced by sc2_ for clarification
Enables Kraken to work on Monkeypox with addition of target_org variable
Removes all String to File coercion for kraken_report outputs
Adds target_org output toread_QC_trim workflows
Changes all workflows to have new import paths
Changes all workflows to take in reference genome and organism variables
Changes all workflows to have optional output values
This broke the GitHub actions; I tried to fix them but I think I'm a little out of my depth here at the moment.
This PR also closes #151 because it will no longer be an issue; s-gene calculations are now performed only once.
This PR enables the ability to analyze MPXV genomes with the intent to be able to easily add other viral pathogens in the future, like HIV, WNV, etc.
stats_n_coverageinto a new task in a quality_control folderconsensus_qcinto a new task in the quality_control folderGENOME_LENto be calculated from the reference genome if one is provided; the default is SC2 length. This will allow for proper calculation of percent_genome_coverage metricsfastq_scantasks into quality_control folderfastqctasks into quality_control folderqc_utilstask filetask_sc2_genome_coverage.wdlsc2_for clarificationtarget_orgvariablekraken_reportoutputstarget_orgoutput toread_QC_trimworkflowsreference genomeandorganismvariablesThis broke the GitHub actions; I tried to fix them but I think I'm a little out of my depth here at the moment.
This PR also closes #151 because it will no longer be an issue; s-gene calculations are now performed only once.