Harshil Patel

I have done something similar in the nanoseq pipeline. Check out the format of the input samplesheet [here](https://nf-co.re/nanoseq/1.1.0/usage#introduction). The important thing is to have a validation script for the samplesheet...

Hi @Rooksie ! Haven't seen this error before but looks like it is coming from here: ``` Command error: mkdtemp(/local_scratch/pbs.87345.pbs02/bcftools.UkuBYp) failed: No such file or directory ``` For some reason,...

You could try to create a `custom.config` with the contents below and pass to the pipeline via `-c`: ``` process { withName: '.*:.*:VARIANTS_IVAR:BCFTOOLS_SORT' { ext.args = '--temp-dir ./' } }...

Hi @junaruga ! Apologies for the late response. It appears I wasn't watching this repo for some reason. Did you mange to fix the issue above?

Closing this but feel free to re-open if the issue persists in version 1.1.0.

Thanks @junaruga. Unfortunately, I don't use Docker but could you maybe try deleting the image and re-running? Sorry, I closed the issue hoping it would be magically fixed. If you...

Re-opened the issue @junaruga and invited you to become a member of the nf-core organisation. Hopefully, this means you will be able to re-open issues in the future as well...

Could be worth asking on the nf-core Slack on the #help channel.

> The error message /bin/bash: .command.run: Permission denied was disappeared. So, first we need to find which part of nextflow or nf-core/nanoseq is needed to be fixed to run the...

Sweet! So you have it working now? Be great if you can post the additional options you needed to use here too.