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sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
MIT License
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Troubleshooting ORFCalling nextflow with Anne #69

Closed gsheynkman closed 3 years ago

gsheynkman commented 3 years ago

Hi @adeslatt, I attempted to run the baby nextflow code to run Transdecoder. I correct a few minor bugs (e.g., lr_orfcalling.nr -> lr_orfcalling.nf). The help message displayed correctly.

The nextflow processing step does appear to be running, and returns error 127.

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When I look at the latest nextflow log, the problem appears to be during DEBUG nextflow.cli.Launcher:

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What I'm wondering is if it is looking for nextflow.config? I had an earlier version of nextflow.config in the directory, which led to problems with display of the help method, so I "stashed" away nextflow.config. But nextflow appears to continue to look for it. Not sure if that has something to do with the issue.

I compared nextflow.config with lr_orfcalling_nextflow.config, and the only difference appears to be pointers to the executors and test configs.

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I also went into the .command.sh file that nextflow is running, and see that there are two Transdecoder commands to run:

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But, when these are run, Transdecoder is not found. So, does that mean we need to add code to have docker install Transdecoder in case it doesn't find it? Or do we need to remember to install Transdecoder before running this code?

I also looked at the aws.config file, and it appears that Transdecoder is not listed. Should we change Transdecoder in the command to ORFtransdecoder?

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gsheynkman commented 3 years ago

Okay - tried changing the TransDecoder command to ORFtransdecoder in the *.nf script, still can't find it.