Closed Vlad-Dembrovskyi closed 2 years ago
With Gen3-DRS input option the pipeline is failing at the moment: https://cloudos.lifebit.ai/public/jobs/6195a5ddfb26cf01dce62a49 https://cloudos.lifebit.ai/public/jobs/619d3eb740695e01e73e9b67
Error message:
No such file: ..../.command.env
Suspicion: It may be this output env(sample_name) that is causing the issue. We had this error before in other pipelines. https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/217e202cab3264c9d2d4cafe80b2476a2d837a85/main.nf#L479
env(sample_name)
David suggested change env(...) format of output to stdout (example) Basically echo the desired value to stdout, and capture stdout. Risc: there may be a lot of stuff printed to stdout.
env(...)
stdout
How will we implement the solution?
Problem
With Gen3-DRS input option the pipeline is failing at the moment: https://cloudos.lifebit.ai/public/jobs/6195a5ddfb26cf01dce62a49 https://cloudos.lifebit.ai/public/jobs/619d3eb740695e01e73e9b67
Error message:
Suspicion: It may be this output
env(sample_name)that is causing the issue. We had this error before in other pipelines. https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/217e202cab3264c9d2d4cafe80b2476a2d837a85/main.nf#L479Solution
David suggested change
env(...)format of output tostdout(example) Basically echo the desired value to stdout, and capture stdout. Risc: there may be a lot of stuff printed to stdout.Implementation
How will we implement the solution?