iraiosub
commented
2 months ago You need to set the environment variable NXF_HOME. NXF_HOME specifies the directory where Nextflow stores its configuration files, logs, and temporary files. By default, Nextflow uses the .nextflow directory in the user’s home directory.
By settingNXF_HOME to a custom path, you can control where Nextflow stores these files, which is useful for managing workflows in shared or cluster environments. So when you are outside your home directory you should explicitly set the NXF_HOME variable to a location of your choice that you can re-use for your sub-sequent runs. You can use sth like export NXF_HOME=full_path_of_your_choice/.nextflow. if you don't set this variable, Nextflow will not see the files stored in the repo. You should also always pull the pipeline before running it.
Also make sure your samplesheet contains full paths to the data, otherwise Nextflow would not find the files. This may be the reson for your second error. I recommend you to check the Nextflow documentation or consult your system administrator on how to set it up on your system if this is your first time working with Nextflow pipelines.
huipan1973
I am running the test of Riboseq-flow on the clusters. I can successfully run the test in my home directory, where the riboseq-flow repo is stored. However, when I change the working directory and run the test, it gives an error saying that a file (multiqc_config.yaml) in the riboseq-flow repo can’t be found. But that file is in the correct location specified by the command shown in the error message. I don’t know what’s going on. It looks like the pipeline can’t work on two directories at the same time.
Also, when running the real data, it gives an error saying the "file argument" can't be null. Possibly, this is due to the same reason.