nfcore rnaseq using AWSbatch #3440
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adityamahadevaniyer
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Hi nfcore. Does anyone have a workable config file to run the latest version of nf-core/rnaseq on AWSBatch. I am relatively new, so if someone can write down the command that I can paste or use in a text file , that would be great.
I think the latest config do not have AWS batch, so I have been trying using the command as given below
nextflow run nf-core/rnaseq
-profile test,docker
—outdir ‘s3://path’
-w ‘s3://path’
old version had awsbatch support, so I have also tried running this using my files.
nextflow run nf-core/rnaseq -r 1.4.2
-profile awsbatch —awsqueue ‘queueid’ —awsregion <> —reads ‘s3:/path/*_{1,2}.fastq.gz’
—genome GRCm38 —outdir ‘s3://path/’
-w ‘s3://path/’
The error I am getting is — Unexpected error stackoverflow error
If you have been already addressed the issue somewhere, please paste the links in the reply. I would be happy to get the answers there.
Thank you!
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