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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Pipeline documentation: standardisation with nf-core template architecture
…plate-merge-3.4.1 # Conflicts: # .github/workflows/awsfulltest.yml # .github/workflows/awstest.yml # .github/workflows/ci.yml # .nf-core.yml # README.md # assets/multiqc_config.yml # assets/nf-core-deepmutscan_logo_light.png # assets/schema_input.json # docs/images/nf-core-deepmutscan_logo_dark.png # docs/images/nf-core-deepmutscan_logo_light.png # docs/output.md # docs/usage.md # nextflow.config # ro-crate-metadata.json # workflows/deepmutscan.nf
test_full now runs the GID1A dataset from ENA (PRJEB110196), and the seqdepth rarefaction uses a geometric depth grid instead of 40 even steps.
The GID1A AlphaFold model now lives on the deepmutscan branch of nf-core/test-datasets instead of in assets/.
Add full-size test and finer seqdepth grid
MaximilianStammnitz
added
the
documentation
Docs, contributors and citations ahead of release review
Same-page links in srcdoc frames navigated to the parent report, nesting it inside MultiQC on every click. Fixes #75.
Fix/report frame anchor links
Docs: README and CHANGELOG follow-ups
Conflicts resolved: - modules.json, tests/nextflow.config: keep dev (pipeline modules and test params) - utils_nfcore_deepmutscan_pipeline: keep the template's UTILS_NFSCHEMA_PLUGIN form - container lock configs, ro-crate-metadata.json: regenerated below
- nf-core modules update --all: fastqc 0.12.1 -> 0.13.0, samtools 1.23.1 -> 1.24 - nf-core subworkflows update --all: utils_nextflow_pipeline, utils_nfcore_pipeline, utils_nfschema_plugin - regenerate ro-crate-metadata.json
subworkflows update --all pulled it ahead of the pinned nf-schema plugin: the newer subworkflow needs nf-schema 3.0.0 (single-argument paramsSummaryLog and paramsHelp) while nextflow.config pins 2.5.1, so every run died at init with 'Missing process or function paramsSummaryLog'. The utils_nextflow_pipeline and utils_nfcore_pipeline updates are kept - those are what issue #66 needed.
Important! Template update for nf-core/tools v4.1.0
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Do not merge! This is a PR of
devcompared to theTEMPLATEbranch for whole-pipeline reviewing purposes.Changes should be made to
devand this PR should not be merged!