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As Shane requested, it should be possible to run ASCC so that one run corresponds to one curation ticket. The pipeline would take in a primary assembly FASTA file, haplotigs FASTA file and the organellar FASTA files at once, and then run the required things (e.g. FCS-GX, Tiara and sanger-tol/blobtoolkit) with all of them, creating separate outputs for each of FASTA file. So basically it looks like there should be another workflow that is a wrapper around the current main workflow.
Dealing with FCS-GX would be a special case: it would be good to run FCS-GX with all assembly components (primary assembly, haplotigs and organellar sequences) in a single job, in order to spend less compute time and resources on repeatedly copying the FCS-GX database to over to /tmp. Every run of FCS-GX starts with copying the database to /tmp, so currently the copying of the database to /tmp is done all over again with every component of the assembly
The text was updated successfully, but these errors were encountered:
Description of feature
As Shane requested, it should be possible to run ASCC so that one run corresponds to one curation ticket. The pipeline would take in a primary assembly FASTA file, haplotigs FASTA file and the organellar FASTA files at once, and then run the required things (e.g. FCS-GX, Tiara and
sanger-tol/blobtoolkit
) with all of them, creating separate outputs for each of FASTA file. So basically it looks like there should be another workflow that is a wrapper around the current main workflow.Dealing with FCS-GX would be a special case: it would be good to run FCS-GX with all assembly components (primary assembly, haplotigs and organellar sequences) in a single job, in order to spend less compute time and resources on repeatedly copying the FCS-GX database to over to
/tmp
. Every run of FCS-GX starts with copying the database to/tmp
, so currently the copying of the database to/tmp
is done all over again with every component of the assemblyThe text was updated successfully, but these errors were encountered: