Closed jloubser closed 2 years ago
Hopefully, this one was resolved in our discussion yesterday?
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.
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
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.
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