Open Mia0509 opened 8 months ago
I think we should merge #177 first and maybe have a look on how to deal with this params validation with the nf-validation plugin.
nf-core lint
overall result: Failed :x:Posted for pipeline commit ce2cd3a
+| ✅ 148 tests passed |+
!| ❗ 1 tests had warnings |!
-| ❌ 10 tests failed |-
PR checklist
This PR fix the point 1 of issue #62, where providing a single number for
--bin_size
in the command line make the pipeline fail (due to parameter validation expecting a String and a single number is considered as an Integer (even when adding quote in command line, Unix strip those automatically)).The fix is applied for the other parameters with same validation error (
res_dist_decay
,res_tads
andres_compartments
).Here's what was done:
nextflow_schema.json
. It happens inWorkflowHic.groovy
with the digestion parameters check as the functioncheckParamIntList
..splitCsv().flatten()
on the parameter if it's an Integer, which gives a error otherwise. This is called inhic.nf
when combining all maps resolution.schema_ignore_param
in all the configs file, so the original validation don't throw an error and the parameters are still referred in the schema.Hope this little fix can be useful!