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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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GATK/Nextflow Java environment differences #70

Closed jloubser closed 2 years ago

jloubser commented 2 years ago

GATK requires java 8, but Nextflow at least Java 11. One can't launch Nextflow when you've activated the mtbseq-env. But when you run the pipeline from the base environment it runs up until BATCH_ANALYSIS:TBFULL and then gives an error at: Command executed: gatk-register GenomeAnalysisTK.jar

abhi18av commented 2 years ago

Hopefully, this one was resolved in our discussion yesterday?

jloubser commented 2 years ago

Almost, I opened up a discussion in the general tab you created. I can't start Nextflow when that environment is activated. Is there a way around that..? Mtbseq worked but the Amend and Joint and another one is empty. I suspect this is Mtbseq-specific and not this pipeline.

abhi18av commented 2 years ago

Ah no - this is related to #72

@jloubser , if you want to run via the nextflow layer, then please deactivate the mtbseq-nf-env since the -profile conda will instruct nextflow to automatically pick that env for executing mtbseq.

But for executing NF itself, please use the env with Java-11

abhi18av commented 2 years ago

Mtbseq worked but the Amend and Joint and another one is empty. I suspect this is Mtbseq-specific and not this pipeline.

Yeah, that's MTBseq specific.