Disha/nf_lint_test

.github/workflows/linting.yaml

@@ -1,5 +1,5 @@
 name: Run Linting
-on: [push, pull_request]
+on: {}
 
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity

.github/workflows/nf-test.yaml

@@ -1,5 +1,16 @@
 name: NF Tests
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "**/meta.yml"
+
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - "**/meta.yml"
 
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity

modules/ensembl/annotation/dumpanno/main.nf

@@ -24,7 +24,7 @@ process ANNOTATION_DUMPANNO {
 
     output:
         tuple val(db), val("functional_annotation"), path("*.json"), emit: functional_annotation
-        path "versions.yml", emit: versions
+        path "versions.yml", emit: versions, topic: versions
 
     when:
         task.ext.when == null || task.ext.when

modules/ensembl/annotation/dumpanno/meta.yml

@@ -1,51 +1,41 @@
----
-name: "annotation_dumpanno"
-
-description: This module is used to dump the functional annotation of a genome from core databases.
-
+name: annotation_dumpanno
+description: This module is used to dump the functional annotation of a genome from
+  core databases.
 keywords:
-  - container
-  - core_database
-  - docker
-  - ensembl-legacy-scripts
-  - fasta
-
+- container
+- core_database
+- docker
+- ensembl-legacy-scripts
+- fasta
 tools:
-  - "annotation":
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      description: "This module handles all annotation-related interactions with the core database, including annotation dumping and processing"
-      license: ['Apache License version 2.0']
-
+- annotation:
+    homepage: https://github.com/Ensembl/nextflow_modules
+    description: This module handles all annotation-related interactions with the
+      core database, including annotation dumping and processing
+    licence:
+    - Apache License version 2.0
 input:
-  # Only when we have meta
-  - meta:
-        type: map
-        description: |
-          A meta map including 'core database information'.
-          e.g. [ id:'db_name', server_details:[ host:'db' ] ]
-        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+- db:
+    type: map
+    description: Channel element db.
 output:
-  - meta:
-      type: map
-      description: |
-        Database containing meta information.
-        e.g. [ id:'db_name', server_details:[ host:'db' ] ]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
-  - functional_annotation.json:
-      type: map
-      description: |
-        Functional annotation file containing biotypes.
-        e.g [ db:'database name', file("*.json") ]
-      pattern: ".json"
-
-  - versions:
+  functional_annotation:
+  - - db:
+        type: map
+        description: Channel element db.
+    - functional_annotation:
+        type: string
+        description: Channel element functional_annotation.
+    - '*.json':
+        type: file
+        description: Channel element *.json.
+        pattern: '*.json'
+  versions:
+  - versions.yml:
       type: file
       description: File containing software versions.
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
+- '@ensembl-dev'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'

modules/ensembl/annotation/dumpanno/tests/main.nf.test

@@ -21,6 +21,8 @@ nextflow_process {
 
     tag "annotation"
     tag "annotation/dumpanno"
+    tag "modules_ensembl"
+    tag "modules"
 
 
     test("Dump functional annotation ") {

modules/ensembl/database/dbfactory/meta.yml

@@ -1,41 +1,43 @@
----
-name: "database_dbfactory"
-description: Generate a list of one or more databases plus some associated meta table information.
-
+name: database_dbfactory
+description: Generate a list of one or more databases plus some associated meta table
+  information.
 keywords:
-  - container
-  - core_database
-  - docker
-  - database
-  - ensembl-genomio
-
+- container
+- core_database
+- docker
+- database
+- ensembl-genomio
 tools:
-  - database:
-      description: "Modules which function to read or write information from core databases."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
-
+- database:
+    description: Modules which function to read or write information from core databases.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 input:
-  - server:
-      type: map
-      description: "Groovy Map containing mysql server host, port, user and password 
-        meta and file of JSON database filter information."
-        e.g. [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
-  - filtermap:
+- - server:
       type: map
-      description: "Prefix to filter core databases. [default: none]"
+      description: 'Groovy Map containing MySQL server host, port, user and password
 
+        metadata, plus the JSON database filter information.
+
+        Example: [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
+
+        '
+  - filter_map:
+      type: map
+      description: Channel element filter_map.
 output:
-  - dbs_meta_json:
+  dbs_meta_json:
+  - dbs.json:
       type: file
-      description: "JSON file containing database metadata."
-      pattern: "dbs.json"  
-  - versions:
+      description: JSON file containing database metadata.
+      pattern: dbs.json
+  versions:
+  - versions.yml:
       type: file
       description: File containing information on module software version
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk

modules/ensembl/download/assemblydata/meta.yml

@@ -1,46 +1,135 @@
----
-name: "download_assemblydata"
-description: Generate a list of one or more databases plus some associated meta table information.
-
+name: download_assemblydata
+description: Generate a list of one or more databases plus some associated meta table
+  information.
 keywords:
-  - ensembl-genomio
-  - container
-  - docker
-  - download
-  - genome
-  - gzip
-  - INSDC
-
+- ensembl-genomio
+- container
+- docker
+- download
+- genome
+- gzip
+- INSDC
 tools:
-  - download:
-      description: "Modules which function to download information or various data from externally hosted resources."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
-
+- download:
+    description: Modules which function to download information or various data from
+      externally hosted resources.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing A single INSDC GCA or NCBI 'amended' GCF genome assembly accession meta information.
-        e.g. `[ accession:'GCA_000000000.1' ]`
+- meta:
+    type: map
+    description: 'Groovy Map containing A single INSDC GCA or NCBI ''amended'' GCF
+      genome assembly accession meta information.
+
+      e.g. `[ accession:''GCA_000000000.1'' ]`
 
+      '
 output:
-  - min_set:
-      type: map
-      description: "Groovy Map including various genome assembly data files (.txt, .fna, .gbff) into compressed Gzip archives."
-        e.g. [ accession:'GCA_000000000.1', file("*_assembly_report.txt"), file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
-      pattern: (*.txt, *.fna.gz, *.gbff.gz)
-  - opt_set:
-      type: map
-      description: "Groovy Map including various genome assembly data files (.txt, .faa, .gff) into compressed Gzip archives."
-        e.g. [ accession:'GCA_000000000.1', file("*_assembly_report.txt"), file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
-      pattern: (*.txt, *.fna.gz, *.gbff.gz)
-  - versions:
+  min_set:
+  - - meta:
+        type: map
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_assembly_report.txt':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_genomic.fna.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_genomic.gbff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+  opt_set:
+  - - meta:
+        type: map
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_genomic.gff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_protein.faa.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_genomic.gbff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+  versions:
+  - versions.yml:
       type: file
       description: File containing information on module software version
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk