Fix lintting errors

dwells-eit · dwells-eit · commit 3a8ca31714b7 · 2025-10-28T13:12:27.000Z
- Correct meta.yml output
- tag all modules included in tests
- remove final TODOs
diff --git a/modules/nf-core/autocycler/cluster/environment.yml b/modules/nf-core/autocycler/cluster/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/cluster/tests/main.nf.test b/modules/nf-core/autocycler/cluster/tests/main.nf.test
@@ -5,8 +5,9 @@ nextflow_process {
     process "AUTOCYCLER_CLUSTER"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
+    tag "autocycler/compress"
     tag "autocycler/cluster"
 
     test("sarscov2 - assembly - fasta") {
diff --git a/modules/nf-core/autocycler/combine/environment.yml b/modules/nf-core/autocycler/combine/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/combine/meta.yml b/modules/nf-core/autocycler/combine/meta.yml
@@ -35,7 +35,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/consensus_assembly.fasta":
+      - "$prefix/consensus_assembly.fasta":
           type: file
           description: Consensus genome sequence generated by Autocycler.
           pattern: "*/consensus_assembly.fasta"
@@ -47,21 +47,22 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/consensus_assembly.gfa":
+      - "$prefix/consensus_assembly.gfa":
           type: file
           description: Consensus assembly graph generated by Autocycler.
-          pattern: "*/consensus_assembly.gfa"
+          pattern: "$prefix/consensus_assembly.gfa"
           ontologies:
-            - edam: "http://edamontology.org/format_3975" #GFA1  stats:
+            - edam: "http://edamontology.org/format_3975" #GFA1
+  stats:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/consensus_assembly.yaml":
+      - "$prefix/consensus_assembly.yaml":
           type: file
           description: Run statistics for the combine step.
-          pattern: "*/consensus_assembly.yaml"
+          pattern: "$prefix/consensus_assembly.yaml"
           ontologies:
             - edam: "http://edamontology.org/format_3750" # YAML
   versions:
diff --git a/modules/nf-core/autocycler/combine/tests/main.nf.test b/modules/nf-core/autocycler/combine/tests/main.nf.test
@@ -5,8 +5,12 @@ nextflow_process {
     process "AUTOCYCLER_COMBINE"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
+    tag "autocycler/compress"
+    tag "autocycler/cluster"
+    tag "autocycler/trim"
+    tag "autocycler/resolve"
     tag "autocycler/combine"
 
     test("sarscov2 - assemblies -fasta") {
diff --git a/modules/nf-core/autocycler/compress/environment.yml b/modules/nf-core/autocycler/compress/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/compress/meta.yml b/modules/nf-core/autocycler/compress/meta.yml
@@ -38,10 +38,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/*.gfa":
+      - "$prefix/*.gfa":
           type: file
           description: Assembly graph files ready for clustering.
-          pattern: "*/*.gfa"
+          pattern: "$prefix/*.gfa"
           ontologies:
             - edam: "http://edamontology.org/format_3975" #GFA1
 
@@ -51,7 +51,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/*.yaml":
+      - "$prefix/*.yaml":
           type: file
           description: Summary statistics generated during compression.
           pattern: "*/*.yaml"
diff --git a/modules/nf-core/autocycler/compress/tests/main.nf.test b/modules/nf-core/autocycler/compress/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "AUTOCYCLER_COMPRESS"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
     tag "autocycler/compress"
 
diff --git a/modules/nf-core/autocycler/resolve/environment.yml b/modules/nf-core/autocycler/resolve/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/resolve/main.nf b/modules/nf-core/autocycler/resolve/main.nf
@@ -36,12 +36,7 @@ process AUTOCYCLER_RESOLVE {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-
     touch 3_bridged.gfa
     touch 4_merged.gfa
     touch 5_final.gfa
diff --git a/modules/nf-core/autocycler/resolve/meta.yml b/modules/nf-core/autocycler/resolve/meta.yml
@@ -40,7 +40,8 @@ output:
           description: Assembly graph with bridges resolved.
           pattern: "3_bridged.gfa"
           ontologies:
-            - edam: "http://edamontology.org/format_3975" #GFA1  merged:
+            - edam: "http://edamontology.org/format_3975" #GFA1
+  merged:
     - - meta:
           type: map
           description: |
@@ -51,7 +52,8 @@ output:
           description: Merged assembly graph after bridging.
           pattern: "4_merged.gfa"
           ontologies:
-            - edam: "http://edamontology.org/format_3975" #GFA1  resolved:
+            - edam: "http://edamontology.org/format_3975" #GFA1
+  resolved:
     - - meta:
           type: map
           description: |
@@ -62,7 +64,8 @@ output:
           description: Final resolved assembly graph.
           pattern: "5_final.gfa"
           ontologies:
-            - edam: "http://edamontology.org/format_3975" #GFA1  versions:
+            - edam: "http://edamontology.org/format_3975" #GFA1
+  versions:
     - "versions.yml":
         type: file
         description: File containing software versions
diff --git a/modules/nf-core/autocycler/resolve/tests/main.nf.test b/modules/nf-core/autocycler/resolve/tests/main.nf.test
@@ -5,8 +5,11 @@ nextflow_process {
     process "AUTOCYCLER_RESOLVE"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
+    tag "autocycler/compress"
+    tag "autocycler/cluster"
+    tag "autocycler/trim"
     tag "autocycler/resolve"
 
     test("sarscov2 - assemblies - fasta") {
diff --git a/modules/nf-core/autocycler/subsample/environment.yml b/modules/nf-core/autocycler/subsample/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/subsample/main.nf b/modules/nf-core/autocycler/subsample/main.nf
@@ -9,8 +9,6 @@ process AUTOCYCLER_SUBSAMPLE {
         'biocontainers/autocycler:0.5.2--h3ab6199_0' }"
 
     input:
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(reads)
     val genome_size
 
diff --git a/modules/nf-core/autocycler/subsample/meta.yml b/modules/nf-core/autocycler/subsample/meta.yml
@@ -39,7 +39,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*/*.fastq.gz":
+      - "$prefix/*.fastq.gz":
           type: file
           description: Subsampled reads produced by Autocycler.
           pattern: "*/*.fastq.gz"
diff --git a/modules/nf-core/autocycler/subsample/tests/main.nf.test b/modules/nf-core/autocycler/subsample/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     config "./nextflow.config"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
     tag "autocycler/subsample"
 
diff --git a/modules/nf-core/autocycler/trim/environment.yml b/modules/nf-core/autocycler/trim/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::autocycler=0.5.2"
diff --git a/modules/nf-core/autocycler/trim/meta.yml b/modules/nf-core/autocycler/trim/meta.yml
@@ -40,7 +40,8 @@ output:
           description: Trimmed assembly graphs emitted by Autocycler.
           pattern: "*.gfa"
           ontologies:
-            - edam: "http://edamontology.org/format_3975" #GFA1  stats:
+            - edam: "http://edamontology.org/format_3975" #GFA1
+  stats:
     - - meta:
           type: map
           description: |
diff --git a/modules/nf-core/autocycler/trim/tests/main.nf.test b/modules/nf-core/autocycler/trim/tests/main.nf.test
@@ -1,14 +1,14 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test autocycler/trim
 nextflow_process {
 
     name "Test Process AUTOCYCLER_TRIM"
     script "../main.nf"
     process "AUTOCYCLER_TRIM"
 
     tag "modules"
-    tag "modules_"
+    tag "modules_nfcore"
     tag "autocycler"
+    tag "autocycler/compress"
+    tag "autocycler/cluster"
     tag "autocycler/trim"
 
     test("sarscov2 - assemblies - fasta") {
diff --git a/modules/nf-core/autocycler/trim/tests/main.nf.test.snap b/modules/nf-core/autocycler/trim/tests/main.nf.test.snap
@@ -192,59 +192,6 @@
         },
         "timestamp": "2025-10-28T10:57:59.014535177"
     },
-    "sarscov2 - bam - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "2_trimmed.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "2_trimmed.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,9d6f2f1409574f288a085c66ba884cb7"
-                ],
-                "gfa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "2_trimmed.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "2_trimmed.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,9d6f2f1409574f288a085c66ba884cb7"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.4"
-        },
-        "timestamp": "2025-10-28T10:50:43.693655569"
-    },
     "sarscov2 - assemblies -fasta - stub": {
         "content": [
             {
