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Benson-Genomics-Lab / TRF

Tandem Repeats Finder: a program to analyze DNA sequences
https://tandem.bu.edu/trf/trf.html
GNU Affero General Public License v3.0
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TRF v4.10.0 on miniconda #13

Open MaestSi opened 2 years ago

MaestSi commented 2 years ago

Dear all, I'm currently integrating TRF in a NextFlow pipeline. Although I've been previously able to use TRF v4.0.9 successfully outside of such framework, it seems I am now facing an issue due to non zero exit status in absence of any errors. In fact, NextFlow is using the exit code to evaluate whether the pipeline execution should stop or not, and it stops when the exit status is not 0. I found in the README: "TRF now has an exit status of 0 on success, and non-zero otherwise. Previously, TRF would have a non-zero exit status which was to be interpreted by the user as the number of TRs processed.". Based on this sentence, I think having a conda v4.10.0 installation for TRF should solve the issue. I already tried compiling from source, but with no success. Could you please update the conda version? Thanks, Simone

xiekunwhy commented 2 years ago

+1

MaestSi commented 2 years ago

For anyone interested in solving the issue (although indirectly): https://github.com/nextflow-io/nextflow/issues/2992