Comments (3)
erikrikarddaniel
commented on July 24, 2024
2
This is fundamental in #magmap. We take either a set of user-supplied genomes that is sketched, a set of ready-made sketches (e.g. GTDB) or both, then submit the selected set to mapping. Basically the whole pipeline in version 1.0, relatively close to release.
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jfy133
commented on July 24, 2024
Ehehehe nf-core/taxprofiler#404
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jfy133
commented on July 24, 2024
But that PR has been abandoned... but I think this is a good case for a common subworkflow :D
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Related Issues (20)
- NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF fails when all genomes classified by ANI screening step HOT 4
- CHECKM_LINEAGEWF failing with exit status 1 HOT 7
- Error in executing PROKKA HOT 4
- Bins in CheckM summary do not match bins in bin depths summary HOT 7
- add diamond support to mag
- Improve documentation on the effects of completeness/contamination filters
- Replace CheckM with CheckM2 HOT 1
- Pipeline completed sucessfully, but with errored process(es) HOT 1
- CAT_DB process has harcoded CAT subdirectory names HOT 1
- List of tool versions HOT 1
- Skipping NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_ALIGN HOT 5
- Allow Prodigal to create a gbk file instead of the gff
- Enter at postbinning stage HOT 9
- Add module pyrodigal
- Upgrade gtdbtk to version 2.4.0 and use reference data release220
- Update the URL for --genomad_db in docs HOT 1
- Pipeline fails with mag_depth script error when bins are empty HOT 2
- GTDBTK_CLASSIFYWF process does not put the summary.tsv file in the output directory HOT 1
- MAG_DEPTHS_PLOT fails if only a single bin is produced HOT 2
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