Comments (10)
I think that was 0.30.2, now with 0.31.0 the error is gone ?!
from tools.
Though perhaps the linting should check for the new format and throw a warning / error about the old?
from tools.
Either way, we should definitely be using the new syntax for all pipelines now.
from tools.
it will stay for a while as a warning, but I agree with Phil better to switch to the new syntax also because it's more flexible.
from tools.
I vote for just the new.
But maybe put that as a warning instead of an error if it's using the old one
from tools.
+1 for just supporting the new if we need to.
Note that the error there is from nextflow though, not the linting. Should probably print the newlines in that so that it's easier to read...
`nextflow config` returned non-zero error code: %s,
%s', 1, b"ERROR ~ Unable to parse config file: '/home/alex/IDEA/nf-core/ICGC-featureCounts/nextflow.config'
Compile failed for sources FixedSetSources[name='/groovy/script/ScriptACEE592A55CA6E05E4ED54DBAB544DAD']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/groovy/script/ScriptACEE592A55CA6E05E4ED54DBAB544DAD: 26: expecting '}', found ':' @ line 26, column 12.
.withName:fetch_encrypted_s3_url {
^
1 error
What version of nextflow is installed? It could be that the linting itself is fine..
from tools.
Can we close this?
from tools.
Yup - will do. I guess the linting is still fine :-)
from tools.
Agreed - I dont know when this will be not just a warning in Nextflow but an actual error message ? @pditommaso may know when this is the case ;-)
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Done in #104
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Related Issues (20)
- Unhelpful error message in nf-core download when container registry is not defined or is wrong HOT 2
- logo generation is inconsistent between github actions runners and local execution
- Schema lint: Handle exceptions for `TypeError`s
- Add option for custom child-template repo HOT 1
- Lint for `assertAll` in `main.nf.test` files
- Positional args warning is misleading
- Print warning if an nf-core module no longer exists.
- Broken link: schema_params HOT 1
- Add a suggestion to re-trigger nf-test when patching a modules
- nf-core download OperationalError: disk I/O error HOT 1
- `nf-core subworkflows test` `--profile` flag doesn't like specifying `docker` or `conda`
- Replace `check_max` with `resourceLimits`
- Renaming job name in linting comment workflow HOT 1
- Combining linting and linting-comment workflows
- Nf-core workflow version update HOT 1
- Subworkflow installation bug
- Update linting to support to changes introduced in `nf-schema` HOT 2
- ToDo: Refactor SyncedRepo class and its subclasses ModulesRepo and WorkflowRepo
- nf-core should support private repos that are not on GitHub HOT 2
- Using the nfcore/tools docker image gets permission denied now
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