Closed rlancaster96 closed 5 months ago
When running with singularity, trimmomatic can't be found because java jar file wasn't added to path. I couldn't add it as an environmental variable.
I modified the nextflow script call for trimmomatic and the issue was solved.
trimmomatic changed tojava -jar /bin/trimmomatic.jar.
trimmomatic
java -jar /bin/trimmomatic.jar.
This means the script will be executable with singularity but may no longer be executable in a conda environment.
When running with singularity, trimmomatic can't be found because java jar file wasn't added to path. I couldn't add it as an environmental variable.
I modified the nextflow script call for trimmomatic and the issue was solved.
trimmomaticchanged tojava -jar /bin/trimmomatic.jar.This means the script will be executable with singularity but may no longer be executable in a conda environment.