TheiaCoV Flu optimizations #749
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…tements, moved read1/2 bash variable lines outside of irma config block
…to set DEL_TYPE to DEL by default instead of old default of NNN; added minimum_read_length input param w default of 75 to match theiacov default; added debugging statements; added 3 outputs for debugging
…s, no longer an issue as of IRMA 1.1.3; added associative arrays/dictionaries for FluA and FluB for formatting; added logic for renaming amended_consensus/ FASTA files
…lurality_consensus_assemblies; task_irma.wdl: added minimum_average_consensus_allele_quality input and defaulted to 10 as this is conservative and used for ONT and ILMN; created dictionaries for ordering FluA and FluB segments in proper largest to smallest orders for concatenated assembly files; updated logic for creating concatenated assembly file; added logic for outputting amended_consensus FASTA files for individual segment File outputs; updated logic for creating padded FASTA files (both for individual segs and multiFASTA and concatenated FASTA) to use amended_consensus FASTA files as source
…ous bases, exposed to user. New outputs of concatenated fasta, padded and unpadded. Debug message changes for less confusion.
…anism parameters subwf. tested with FluA and B w miniwdl successfully
…assembly; changed theiacov_illumina_pe workflow to set this default value separately for ivar and irma via select_first statements; also output this value based on either user selected value, or that reported by irma, or default of 100. added new output to flu_track subwf. tested successfully with miniwdl
…pport and set default to 50 in flu_track call block. Added 3 outputs 1) irma_min_consensus_support_threshold 2) irma_assembly_fasta_concatenated 3) irma_assembly_fasta_concatenated_padded. Tested successfully with miniwdl
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Draft for now, will fill out later
This PR closes #676
🗑️ This dev branch should NOT be deleted after merging to main. Check with Curtis prior to deletion.
🧠 Summary
⚡ Impacted Workflows/Tasks
This PR may lead to different results in pre-existing outputs: Yes/No
This PR uses an element that could cause duplicate runs to have different results: Yes/No
🛠️ Changes
⚙️ Algorithm
➡️ Inputs
⬅️ Outputs
🧪 Testing
Suggested Scenarios for Reviewer to Test
🔬 Final Developer Checklist
workflows_overviewtables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"🎯 Reviewer Checklist