Anders Sune Pedersen

Thanks for reporting this, @famosab. I feel like this situation should have been covered by plugin nf-validation. The version of nf-validation is not fixed in Sarek v3.4 (it will be...

> I think it is the fact we only check for uniqueness with lane > > https://github.com/nf-core/sarek/blob/6aeac929c924ba382baa42a0fe969b4e0e753ca9/assets/schema_input.json#L48 > > but not individually. You reckon that we should also require that...

So far this PR seems like it is adding some stuff and not refactoring 😄 Anyways, linter says "Param modules_testdata_base_path from nextflow config not found in nextflow_schema.json"

In [4575cba](https://github.com/nf-core/sarek/pull/1422/commits/4575cbab5415212f62e2e929343b04b3859f2d58), then full-test is still not running on awsbatch :-/ I still get: ``` ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions.hg38.bed)' Caused by: The user value contains invalid...

I just ran `nextflow run main.nf -profile test_cache,use_gatk_spark,docker --outdir foo`

@FriederikeHanssen : Was this observed on `master` or `dev`?

With nf-shema, the problem can be solved by adding the following to `nextflow.config` : ``` "if": { "properties": { "tools": { "pattern": ".*sentieon_dedup.*" } } }, "then": { "properties": {...

Looks very good 👏👏 What about CI-tests covering this new functionality?

Thanks for the updates 🙌 Concerning CI-tests for this new functionality, I see we already have [this](https://github.com/nf-core/sarek/blob/6e2325a7dd882f433b04d9089dccf35214548e4a/tests/test_cnvkit.yml#L112) pytest of the germline subworkflow of cnvkit, and it runs `CNVKIT_EXPORT` and generates...

@DimitrisZisis : Thanks for reporting this. I know that Sarek runs fine over awsbatch, so I guess it should also be possible to get it running over AWS Healthomics. Did...