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microbiomedata / metaMAGs

Workflow for metagenome assembled genomes generation.
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Add support for passing a contig name mapping file to mbin.py #29

Closed aclum closed 4 months ago

aclum commented 5 months ago

When NMDC runs workflows where the assembly was generated at JGI the binning workflow needs a mapping file to convert between the assembly fasta file and annotation files. We need to update the workflow such that there is an option to specify --map

related to https://github.com/microbiomedata/metaMAGs/issues/26

Files that can be used to test this: https://data.jgi.doe.gov/search?q=1414320&expanded=IMG_AP-1414320

assembly file: assembly.contigs.fasta mapping file: Ga0597049_contig_names_mapping.tsv

chienchi commented 5 months ago

add --map option not work on assembly file: assembly.contigs.fasta but work on assembly file: Ga0597049_contigs.fna

with map file, the mbin.py workflow will convert the depth coverage info generated from pairedMapped.sam.gz into metabat.depth.mapped file with correct ID.