Closed ilight1542 closed 1 year ago
also note #960 -- changes made to standard metagenomics parameter naming schemes (!!) make sure things are working together prior to merging everything
Hey, @ilight1542 As I cannot push to your private branch, I created a new one here: https://github.com/nf-core/eager/tree/dsl2-metagenomics that combines the complexity filter and your profiling subworkflow into a new subworkflow.
Can we continue on this branch? So that we can both work in parallel :)
@merszym, since the new branch you made removed the tracking of who coded what, I added you as a collaborator to my branch. we should be able to then implement the rest of the subworkflow there and then merge with this PR :)
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 61c8254
+| ✅ 157 tests passed |+
!| ❗ 20 tests had warnings |!
Close pull request as we continue the development on another branch!
Implementation of dsl2 subworkflow (eventually will be implemented as subworkflow of subworkflow, along with #960 and post-processing.
Added functionality: grouping of malt inputs (!!) for parallelized submits across an arbitrary number of fastq files (implementation for outputting needs to be tested/revised)
Also need to figure out which optional parameters for metaphlan2, kraken2, krakenuniq should be included as parameters in nextflow.
PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).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).