Lukas Forer comments

Results 58 comments of


                                            Lukas Forer

Can't use `setup` construct for pipeline testing

Thanks! `setup` is currently not supported by `nextflow_pipeline` testsuites. ATM, it is only supported by `nextflow_process` and `nextflow_workflow`.

Can't use `setup` construct for pipeline testing

I am closing this issue for now. Pipeline tests resemble more of an end-to-end nature, and running dependency processes in the `setup` is therefore not suitable.

Add --target option to nf-test list

Thanks, sounds good! I will try to find some time next week.

Automatic staging of `assets` `bin` and `lib` folders broken

Thanks! I will look into it later this week.

Nextflow Secrets

I have just created a testcase using secrets and it worked as expected. Could you give it a try? Thanks! **test_process.nf** ```nextflow process TEST_PROCESS { publishDir "${params.outdir}" secret 'MY_ACCESS_KEY' output:...

Nextflow Secrets

Thanks, for clarification. I have two points: - I am not sure if this is technically easily possible—we need to avoid overwriting already set secrets or we need to restore...

Process aliases

Thanks for reporting! I link it to issue https://github.com/askimed/nf-test/issues/139

Weird behaviour when Gzipped files are empty

Thanks! I spotted the bug and will fix it (Todo: check content length in https://github.com/askimed/nf-test/blob/552af89191fa0723b9bda3dc1688f1497c7037bb/src/main/java/com/askimed/nf/test/util/FileUtil.java#L111)

Weird behaviour when Gzipped files are empty

Fully agree! Checking the magic byte and throwing an error is definitely the best solution. We should also mark empty files in snapshots, to spot them quickly.

Feature: string search with `.grepLinesGzip()`

Thanks Nicolas, yes, the support of regular expressions is work in progress :) Best, lukas.