add reconstructR workflow #504
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tomkinsc
reviewed
Dec 19, 2023
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| # stage input files | ||
| mkdir -p input_data input_data/vcf input_data/coverage | ||
| /opt/reconstructR/scripts/cp_and_decompress.sh "~{msa_fasta}" input_data/aligned.fasta |
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Can these be put on the PATH in the reconstructr container?
tomkinsc
approved these changes
Dec 19, 2023
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Add new workflow
reconstruct_from_alignmentswhich uses a new tool (reconstructR) to infer disease transmission links based on genomic (consensus genome and intrahost variation) data.The input to this workflow includes an aligned/trimmed BAM and consensus genome (FASTA) per disease case, plus a single reference genome (FASTA, the same one the BAM files are already aligned against). This workflow will perform the necessary intrahost variant calling, multiple alignments, etc, and produce output per the reconstructR tool.