Merge pull request #322 from nf-core/update-taxpasta

Update taxpasta and add taxpasta support for ganon
nf-core · Jul 10, 2023 · 9e99080 · 9e99080
2 parents 31a440c + 80ce81a
commit 9e99080
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Showing 5 changed files with 12 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,9 +33,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-| Tool    | Previous version | New version |
-| ------- | ---------------- | ----------- |
-| MultiQC | 1.13             | 1.14        |
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| MultiQC  | 1.13             | 1.14        |
+| taxpasta | 0.2.3            | 0.4.0       |
 
 ### `Deprecated`
 

diff --git a/modules.json b/modules.json
@@ -224,12 +224,12 @@
                     },
                     "taxpasta/merge": {
                         "branch": "master",
-                        "git_sha": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c",
+                        "git_sha": "ef280893021dd1e877db163966022cabae06dfdb",
                         "installed_by": ["modules"]
                     },
                     "taxpasta/standardise": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ef280893021dd1e877db163966022cabae06dfdb",
                         "installed_by": ["modules"]
                     },
                     "untar": {

diff --git a/modules/nf-core/taxpasta/merge/main.nf b/modules/nf-core/taxpasta/merge/main.nf
diff --git a/modules/nf-core/taxpasta/standardise/main.nf b/modules/nf-core/taxpasta/standardise/main.nf
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
@@ -25,12 +25,6 @@ workflow STANDARDISATION_PROFILES {
 
     //Taxpasta standardisation
     ch_prepare_for_taxpasta = profiles
-                            .filter {
-                                meta, report ->
-                                // TODO: add tool to taxpasta!
-                                    if ( meta['tool'] == 'ganon' ) log.warn "[nf-core/taxprofiler] ganon not yet supported in Taxpasta. Skipping ganon profile for sample ${meta.id}."
-                                    meta['tool'] != 'ganon'
-                            }
                             .map {
                                     meta, profile ->
                                         def meta_new = [:]