Fix linting issues

EBI-Metagenomics · Oct 18, 2024 · dba2496 · dba2496
1 parent 6ed75b3
commit dba2496
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diff --git a/modules/ebi-metagenomics/taxonkit/reformat/environment.yml b/modules/ebi-metagenomics/taxonkit/reformat/environment.yml
@@ -1,5 +1,4 @@
 ---
-name: "taxonkit_reformat"
 channels:
   - conda-forge
   - bioconda

diff --git a/modules/ebi-metagenomics/taxonkit/reformat/meta.yml b/modules/ebi-metagenomics/taxonkit/reformat/meta.yml
@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "taxonkit_reformat"
 description: Reformat lineage in canonical ranks
@@ -15,40 +14,37 @@ tools:
       tool_dev_url: "https://github.com/shenwei356/taxonkit"
       doi: "10.1016/j.jgg.2021.03.006"
       licence: ["MIT"]
+      identifier: biotools:taxonkit
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-
-  - tsv:
-      type: file
-      description: Input TSV file
-      pattern: "*.{tsv,tsv.gz}"
-
-  - taxdb:
-      type: file
-      description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - tsv:
+        type: file
+        description: Input TSV file
+        pattern: "*.{tsv,tsv.gz}"
+  - - taxdb:
+        type: file
+        description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
   - reformat_tsv:
-      type: file
-      description: Reformated output TSV file
-      pattern: "*.{tsv}"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: Reformated output TSV file
+          pattern: "*.{tsv}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@arajkovic"
 maintainers:

diff --git a/modules/ebi-metagenomics/taxonkit/reformat/tests/main.nf.test b/modules/ebi-metagenomics/taxonkit/reformat/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "TAXONKIT_REFORMAT"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_ebimetagenomics"
     tag "taxonkit"
     tag "taxonkit/reformat"