Merge pull request #894 from maxulysse/remove_test_warnings

Remote test warning from nf-core lint
nf-core · Dec 12, 2022 · e48ce04 · e48ce04
2 parents 63822b6 + 4ac0b43
commit e48ce04
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
 - [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff`
+- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to --cnvkit_reference
+- [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt
 
 ### Deprecated
 

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/sarek Methods Description"
 section_href: "https://github.com/nf-core/sarek"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/sarek v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>

diff --git a/modules.json b/modules.json
@@ -10,14 +10,14 @@
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     },
-                    "bcftools/mpileup": {
+                    "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     },
-                    "bcftools/concat": {
+                    "bcftools/mpileup": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
                         "installed_by": ["modules"]
                     },
                     "bcftools/sort": {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -347,7 +347,9 @@
                     "type": "string",
                     "default": null,
                     "fa_icon": "fas fa-file",
-                    "help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch"
+                    "help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch",
+                    "description": "Copy-number reference for CNVkit",
+                    "hidden": true
                 },
                 "pon": {
                     "type": "string",