add new workflow scaffold_and_refine_multitaxa #506
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tomkinsc
reviewed
Jan 30, 2024
| String sample_id | ||
| File reads_unmapped_bam | ||
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| Array[Pair[Int,Array[String]+]] taxid_to_ref_accessions = [ |
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What about HAdV?
There are quite a few, but if we do want to include them:
# HAdV reference genomes, via https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10509&host=human
(129875, ["NC_001460.1"]), # Human mastadenovirus A strain:Huie; serotype:Human adenovirus 12; culture-collection:ATCC:VR-863
(108098, ["NC_011203.1"]), # Human adenovirus B1
(108098, ["NC_011202.1"]), # Human adenovirus B2
(129951, ["NC_001405.1"]), # Human mastadenovirus C serotype:Human adenovirus 2
(130310, ["NC_010956.1"]), # Human mastadenovirus D strain:Hicks; NIAID V-209-003-014; serotype:Human adenovirus 9
(130308, ["NC_003266.2"]), # Human mastadenovirus E strain:vaccine (CL 68578); serotype:human adenovirus 4
(130309, ["NC_001454.1"]), # Human mastadenovirus F strain:Dugan; serotype:Human adenovirus 40
(310540, ["NC_006879.1"]), # Simian adenovirus 1 strain:ATCC VR-195
(1123958, ["NC_017825.1"]), # Chimpanzee adenovirus Y25
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I'll get some proposed edits to this default list from Jillian soon
| reference_fasta = scaffold.scaffold_fasta, | ||
| sample_name = sample_id | ||
| } | ||
| # to do: if pre-impute unambig length > some fraction of ref genome, run ncbi.rename_fasta_header and ncbi.align_and_annot_transfer_single |
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some fraction of ref genome will be a workflow parameter?
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Also, maybe we try Liftoff for annotation transfer (no chain file required—it does the alignment via minimap2).
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Yeah I think that's right... this is all obviously to do at some future stage.
| -f "~{reference_fasta}" "~{reads_aligned_bam}" \ | ||
| | bcftools call \ | ||
| -P 0 -m --ploidy 1 \ | ||
| --threads $(nproc) \ |
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Maybe reserve a core for the system, writes, etc. ($(nproc --ignore=1))?
tomkinsc
approved these changes
Feb 1, 2024
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This PR adds a new workflow called
scaffold_and_refine_multitaxawhich runs scaffold_and_refine on one input sample (contigs + reads) against many reference genomes from different taxa of interest. This is designed to attempt to assemble all taxa of interest for every sample, and will produce partial and empty outputs for all unsuccessful sample x taxon combinations. It is intended for high throughput metagenomic analyses.This includes a few updates to tasks to make them more resilient to empty fasta inputs/outputs:
scaffoldrun_discordancealignment_metrics