Closed scwatts closed 1 month ago
Force pushing latest commit to attempt to cleanly retrigger CI
CI is giving the following error:
ERROR ~ mapping values are not allowed here
in 'reader', line 2, column 109:
... bd13032d9db48ac3fb9e/.command.sh: line 4: samtools: command not ...
^
-- Check script './subworkflows/local/utils_nfcore_oncoanalyser_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf' at line: 106 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
-[nf-core/oncoanalyser] Pipeline completed with errors-
But I can't replicate locally. I'm going to roll back some changes to see if I can isolate the problem.
CI appears to be having issues with a non-stub samplesheet. Adding relevant samplesheet to nf-core/test-datasets and adjust test_stub profile accordingly here. Also force pushing to clean up git history.
Another force push incoming to exclude irrelevant git history
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit f876e18