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StaPH-B / titan

Public health bioinformatics repository for WDL workflows to analyze viral genomes.
GNU Affero General Public License v3.0
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Inconsistencies in samtool version used in tasks #10

Closed jvhagey closed 3 years ago

jvhagey commented 3 years ago

In task_consensus_call.wdl:

task_assembly_metrics.wdl currently uses container: staphb/samtools:1.10

I suggest we make a container that has samtools v1.12 and bwa v0.7.17-r1188 that all these tasks can pull from. Or we can use samtools v1.10 then still pull from staphb/samtools:1.10 for task_assembly_metrics.wdl and then that workflow will have an easy way to see the version of samtools used.

kapsakcj commented 3 years ago

I suggest we make a container that has samtools v1.12 and bwa v0.7.17-r1188 that all these tasks can pull from

and additionally ivar 1.3.1, right?

We could update the existing ivar 1.3.1 dockerfile to include bwa.

And for the variant_call task, I believe the reason it's currently stuck with that container due to it's use of the BED file & GFF file that are included, which the ivar 1.3.1 dockerfile does not have.

Perhaps we could create a new dockerfile that includes everything, and use that for task_consensus_call.wdl

'everything' means:

could call the docker image staphb/ivar:1.3.1_artic20200528

And that is assuming we want to keep the bed & gff files instead of having the user supply them as an input parameter. Either way there's a solution!

jvhagey commented 3 years ago

Per @kevinlibuit the bedfile that is in the staphb/ivar:1.2.2_artic20200528 is incorrect and leading to primers not being trimmed. The issue was brought up on slack. @kevinlibuit also mentioned that Theiagen is moving toward having the genome and bed files not being part of containers, but rather are user input. This would allow the ivar container to be less SC2 specific. Thoughts on removing the bed file and gff file and having them as user input instead? @kapsakcj @k-florek

kapsakcj commented 3 years ago

New dockerfile added: https://github.com/StaPH-B/docker-builds/tree/master/ivar/1.3.1_Titan

Thanks for the pull request, Jill!

Docker image is available https://hub.docker.com/r/staphb/ivar/tags?page=1&ordering=last_updated

docker pull staphb/ivar:1.3.1-titan

Only other addition might be minimap2, but we can add that later if requested