MISO_SASHIMI looks in NXF_HOME subdirectory instead of working directory for output files

[nf-core]

MISO_SASHIMI looks in NXF_HOME subdirectory instead of working directory for output files

[bensouthgate]

Hi @dkoppstein I believe this might be an issue with how the --bam_prefix and --miso_prefix are defined within the modules.config file. I think this will need to be refactored to work on all setups. @valentinoruggieri something like stageInMode = 'copy' might work if the normal stage in approach is not working for MISO.

[dkoppstein]

Not sure if it's the universal solution, but changing ${projectDir} to ${launchDir} as here seems to make it run for me.

[dkoppstein]

I have committed fixes on my fork for this issue and #74, but don't have access to a linux box where I can run the docker version of the test at the moment (only Singularity). Could I ask one of the devs to run the formal docker test, then I could create the PR?

[valentinoruggieri]

@dkoppstein , thank you for your revisions. We tested your fork on docker but we are still getting some problems.
Since the issue only happens when running the pipe using URL, for a temporary solution you can download/clone the pipe and run it (nextflow run main.nf ...)
Keep you updated