[automated] Fix code linting

.nf-core.yml

@@ -1,10 +1,10 @@
 lint:
   files_unchanged:
-  - lib/NfcoreTemplate.groovy
+    - lib/NfcoreTemplate.groovy
   nextflow_config:
-  - config_defaults:
-    - params.phix_reference
-    - params.lambda_reference
+    - config_defaults:
+        - params.phix_reference
+        - params.lambda_reference
 nf_core_version: 3.1.0
 repository_type: pipeline
 template:

assets/multiqc_config.yml

@@ -17,91 +17,91 @@ disable_version_detection: true
 data_format: "yaml"
 
 run_modules:
-- fastqc
-- fastp
-- adapterRemoval
-- custom_content
-- bowtie2
-- busco
-- quast
-- kraken
-- prokka
-- porechop
-- filtlong
+  - fastqc
+  - fastp
+  - adapterRemoval
+  - custom_content
+  - bowtie2
+  - busco
+  - quast
+  - kraken
+  - prokka
+  - porechop
+  - filtlong
 
 ## Module order
 top_modules:
-- "fastqc":
-    name: "FastQC: raw reads"
-    path_filters_exclude:
-    - "*trimmed*"
-- "fastp"
-- "adapterRemoval"
-- "porechop"
-- "filtlong"
-- "fastqc":
-    name: "FastQC: after preprocessing"
-    info: "After trimming and, if requested, contamination removal."
-    path_filters:
-    - "*trimmed*"
-- "bowtie2":
-    name: "Bowtie2: PhiX removal"
-    info: "Mapping statistics of reads mapped against PhiX and subsequently removed."
-    path_filters:
-    - "*_phix_removed.bowtie2.log"
-- "bowtie2":
-    name: "Bowtie2: host removal"
-    info: "Mapping statistics of reads mapped against host genome and subsequently
-      removed."
-    path_filters:
-    - "*_host_removed.bowtie2.log"
-- "kraken":
-    name: "Kraken2"
-    anchor: "Kraken2"
-    target: "Kraken2"
-    doi: "10.1101/gr.210641.116"
-    path_filters:
-    - "*.kraken2_report.txt"
-- "kraken":
-    name: "Centrifuge"
-    anchor: "centrifuge"
-    target: "Centrifuge"
-    doi: "10.1101/gr.210641.116"
-    info: "is a very rapid and memory-efficient system for the classification of DNA
-      sequences from microbial samples. The system uses a novel indexing scheme based
-      on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
-      Note: Figure title"
-    extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
-      format as Kraken. If activated, see the actual Kraken2 results in the section
-      above."
-    path_filters:
-    - "*.centrifuge_kreport.txt"
-- "quast":
-    name: "QUAST: assembly"
-    info: "Assembly statistics of raw assemblies."
-    path_filters:
-    - "*rawassemblies.tsv"
-- "bowtie2":
-    name: "Bowtie2: assembly"
-    info: "Mapping statistics of reads mapped against assemblies."
-    path_filters_exclude:
-    - "*_host_removed.bowtie2.log"
-    - "*_phix_removed.bowtie2.log"
-- "bcftools"
-- custom_content
-- "quast":
-    name: "QUAST: bins"
-    info: "Assembly statistics of binned assemblies."
-    path_filters_exclude:
-    - "*rawassemblies.tsv"
-- "busco":
-    info: "assesses genome assembly and annotation completeness with Benchmarking
-      Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
-      was used, only generic results for the selected domain are shown and only for
-      genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
-      i.e. not for contigs for which no BUSCO genes could be found. Bins for which
-      a specific virus lineage was selected are also not shown."
-- "prokka"
+  - "fastqc":
+      name: "FastQC: raw reads"
+      path_filters_exclude:
+        - "*trimmed*"
+  - "fastp"
+  - "adapterRemoval"
+  - "porechop"
+  - "filtlong"
+  - "fastqc":
+      name: "FastQC: after preprocessing"
+      info: "After trimming and, if requested, contamination removal."
+      path_filters:
+        - "*trimmed*"
+  - "bowtie2":
+      name: "Bowtie2: PhiX removal"
+      info: "Mapping statistics of reads mapped against PhiX and subsequently removed."
+      path_filters:
+        - "*_phix_removed.bowtie2.log"
+  - "bowtie2":
+      name: "Bowtie2: host removal"
+      info: "Mapping statistics of reads mapped against host genome and subsequently
+        removed."
+      path_filters:
+        - "*_host_removed.bowtie2.log"
+  - "kraken":
+      name: "Kraken2"
+      anchor: "Kraken2"
+      target: "Kraken2"
+      doi: "10.1101/gr.210641.116"
+      path_filters:
+        - "*.kraken2_report.txt"
+  - "kraken":
+      name: "Centrifuge"
+      anchor: "centrifuge"
+      target: "Centrifuge"
+      doi: "10.1101/gr.210641.116"
+      info: "is a very rapid and memory-efficient system for the classification of DNA
+        sequences from microbial samples. The system uses a novel indexing scheme based
+        on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
+        Note: Figure title"
+      extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
+        format as Kraken. If activated, see the actual Kraken2 results in the section
+        above."
+      path_filters:
+        - "*.centrifuge_kreport.txt"
+  - "quast":
+      name: "QUAST: assembly"
+      info: "Assembly statistics of raw assemblies."
+      path_filters:
+        - "*rawassemblies.tsv"
+  - "bowtie2":
+      name: "Bowtie2: assembly"
+      info: "Mapping statistics of reads mapped against assemblies."
+      path_filters_exclude:
+        - "*_host_removed.bowtie2.log"
+        - "*_phix_removed.bowtie2.log"
+  - "bcftools"
+  - custom_content
+  - "quast":
+      name: "QUAST: bins"
+      info: "Assembly statistics of binned assemblies."
+      path_filters_exclude:
+        - "*rawassemblies.tsv"
+  - "busco":
+      info: "assesses genome assembly and annotation completeness with Benchmarking
+        Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
+        was used, only generic results for the selected domain are shown and only for
+        genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
+        i.e. not for contigs for which no BUSCO genes could be found. Bins for which
+        a specific virus lineage was selected are also not shown."
+  - "prokka"
 
 custom_data:
   host_removal:
@@ -131,12 +131,12 @@ sp:
 
 ## File name cleaning
 extra_fn_clean_exts:
-- ".bowtie2"
-- "_ar2"
-- "host_removed"
-- "phix_removed"
-- "centrifuge_kreport"
-- "_fastp"
+  - ".bowtie2"
+  - "_ar2"
+  - "host_removed"
+  - "phix_removed"
+  - "centrifuge_kreport"
+  - "_fastp"
 
 ## Prettification
 custom_logo: "mag_logo_mascot_light.png"

ro-crate-metadata.json

@@ -127,11 +127,7 @@
         },
         {
             "@id": "main.nf",
-            "@type": [
-                "File",
-                "SoftwareSourceCode",
-                "ComputationalWorkflow"
-            ],
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "creator": [
                 {
                     "@id": "#[email protected]"
@@ -167,9 +163,7 @@
                 "nanopore",
                 "nanopore-sequencing"
             ],
-            "license": [
-                "MIT"
-            ],
+            "license": ["MIT"],
             "maintainer": [
                 {
                     "@id": "#[email protected]"
@@ -184,22 +178,15 @@
                     "@id": "#[email protected]"
                 }
             ],
-            "name": [
-                "nf-core/mag"
-            ],
+            "name": ["nf-core/mag"],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": [
-                "https://github.com/nf-core/mag",
-                "https://nf-co.re/mag/3.3.0/"
-            ],
-            "version": [
-                "3.3.0"
-            ]
+            "url": ["https://github.com/nf-core/mag", "https://nf-co.re/mag/3.3.0/"],
+            "version": ["3.3.0"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -396,4 +383,4 @@
             "name": "James Fellows Yates"
         }
     ]
-}
+}