add RAM increase for mapping tools

rki-mf1 / clean

A nextflow pipeline for decontamination of short reads, long reads and contigs

BSD 3-Clause "New" or "Revised" License

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add RAM increase for mapping tools #97

Closed hoelzer closed 3 months ago

hoelzer commented 4 months ago

... I ran into problems when using CLEAN for a seal genome (out of RAM on HPC). Thus added error strategies to prevent that.

hoelzer commented 4 months ago

BBDUK unfortunately throws error code 1 when out of RAM... not the usual 130..140 range. So I used error code 1. If for any other reason the tool throws error code 1, it will still try to increase RAM a few times

hoelzer commented 4 months ago

PR is wip... testing minimap2 as well which is still failing for the seal genome

hoelzer commented 4 months ago

Hm wild... also minimapo2 was throwing error code 1 on the cluster so need to use that to catch it and increase resources so the pipeline runs also through with minimap2

hoelzer commented 4 months ago

Ok, this is ready from my side... not super ideal with the error code 1 but works for me

hoelzer commented 3 months ago

I totally forgot about that one. Will test it first again and in case it's still aproblem on the HPC, make a new PR...