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Running the pipeline with primary assembly and haplotigs FASTA files at once #53

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eeaunin opened this issue Jul 26, 2024 · 1 comment · May be fixed by #65
Open

Running the pipeline with primary assembly and haplotigs FASTA files at once #53

eeaunin opened this issue Jul 26, 2024 · 1 comment · May be fixed by #65
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enhancement New feature or request

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@eeaunin
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eeaunin commented Jul 26, 2024

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 assembly

@eeaunin eeaunin added the enhancement New feature or request label Jul 26, 2024
@DLBPointon DLBPointon linked a pull request Nov 13, 2024 that will close this issue
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Included in #65

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