fixed config path for BUSCO when using Singularity

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

GNU General Public License v3.0

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Closed mkierczak closed 4 years ago

mahesh-panchal commented 4 years ago

Issues:

busco exits with exit code 0 on errors.
config.ini path is different in conda, and singularity environments.
- conda: $workDir/conda/busco-<somestring>/config/config.ini
- singularity:/usr/local/config/config.ini
Busco v4.0.2 config.ini has incorrect script path to gff2gbSmallDNA.pl in conda package.
Conda package Busco v4.0.5 contains numerous package conflicts.

mkierczak commented 4 years ago

Resolved issue with BUSCO by migrating to docker hub BUSCO container.

mahesh-panchal commented 4 years ago

That doesn't solve the issue when using the conda environments though. I'm thinking of roling back to a previous version of busco.

mahesh-panchal commented 4 years ago

mahesh-panchal commented 4 years ago

No issues now using Busco 4.0.2 with either conda, or singularity on the other branch. The gff2gbSmallDNA.pl note above seems to be mistake.