Closed muffato closed 9 months ago
nf-core lint
overall result: Failed :x:Posted for pipeline commit 36cd215
+| ✅ 128 tests passed |+
#| ❔ 18 tests were ignored |#
!| ❗ 4 tests had warnings |!
-| ❌ 6 tests failed |-
@muffato Should we attempt to merge this into #83 for testing?
I think there's too much to do for this config file to work. I'd rather merge #83 first, and then work on the config file properly.
Hi,
I've been wondering a lot how to reconcile the parameters that the Nextflow processes use (typically by setting
params.*
andext.args
) and the BTK Yaml file. To avoid redundancy, I think there should be a single source.Here is a proof on concept for using a BTK-style Yaml file as the main configuration mechanism (through Nextflow's native
-params-file
), from which the pipeline takes all its parameters by settingext.args
.This is a draft PR and should remain that way for now. The unit test seems to work, but I've removed some parameter validation and the code would likely crash if some key parameters are missing. I didn't try defining the reads in the Yaml file, so there is still a CSV sample sheet, but that would be the next natural step. Then, to complete the Yaml file that goes into the blobdir, we'd still have to add the software versions (can be done by adding a process that takes
ch_versions
), and some other genome metadata stuff I think.It's just one way of doing. Alternatively the config file could be given through an option like
--btk-config /path/to/yaml
which is parsed and flown into the jobs throughmeta
?Comments welcome 😄
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).