Prettier

Author: pinin4fjords

.nf-core.yml

@@ -1,15 +1,15 @@
 lint:
   files_exist:
-  - conf/modules.config
+    - conf/modules.config
   files_unchanged:
-  - assets/email_template.html
-  - assets/email_template.txt
-  - .gitignore
+    - assets/email_template.html
+    - assets/email_template.txt
+    - .gitignore
   modules_config: false
   multiqc_config: false
   nextflow_config:
-  - config_defaults:
-    - params.ribo_database_manifest
+    - config_defaults:
+        - params.ribo_database_manifest
 nf_core_version: 3.3.2
 repository_type: pipeline
 template:

workflows/rnaseq/assets/multiqc/multiqc_config.yml

@@ -80,41 +80,41 @@ sample_names_replace_exact: true
 
 # Run only these modules
 run_modules:
-- custom_content
-- fastqc
-- cutadapt
-- fastp
-- sortmerna
-- star
-- hisat2
-- rsem
-- umitools
-- salmon
-- kallisto
-- samtools
-- picard
-- preseq
-- rseqc
-- qualimap
-- kraken
+  - custom_content
+  - fastqc
+  - cutadapt
+  - fastp
+  - sortmerna
+  - star
+  - hisat2
+  - rsem
+  - umitools
+  - salmon
+  - kallisto
+  - samtools
+  - picard
+  - preseq
+  - rseqc
+  - qualimap
+  - kraken
 
 # Order of modules
 
 module_order:
-- fastqc:
-    anchor: "fastqc_raw"
-    name: "FastQC (raw)"
-    info: "This section of the report shows FastQC results before adapter trimming."
-    path_filters:
-    - "*_raw*fastqc.zip"
-- cutadapt
-- fastp
-- fastqc:
-    anchor: "fastqc_trimmed"
-    name: "FastQC (trimmed)"
-    info: "This section of the report shows FastQC results after adapter trimming."
-    path_filters:
-    - "*_trimmed*fastqc.zip"
+  - fastqc:
+      anchor: "fastqc_raw"
+      name: "FastQC (raw)"
+      info: "This section of the report shows FastQC results before adapter trimming."
+      path_filters:
+        - "*_raw*fastqc.zip"
+  - cutadapt
+  - fastp
+  - fastqc:
+      anchor: "fastqc_trimmed"
+      name: "FastQC (trimmed)"
+      info: "This section of the report shows FastQC results after adapter trimming."
+      path_filters:
+        - "*_trimmed*fastqc.zip"
 
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible:
@@ -124,10 +124,10 @@ table_columns_visible:
     percent_duplicates: false
 
 extra_fn_clean_exts:
-- ".umi_dedup"
-- "_val"
-- ".markdup"
-- "_primary"
+  - ".umi_dedup"
+  - "_val"
+  - ".markdup"
+  - "_primary"
 
 # Customise the module search patterns to speed up execution time
 #  - Skip module sub-tools that we are not interested in
@@ -160,8 +160,8 @@ sp:
   samtools/idxstats:
     fn: "*.idxstats*"
   kraken:
-  - fn: "*.kraken2.report.txt"
-  - fn: "*.kraken2.report_bracken.txt"
+    - fn: "*.kraken2.report.txt"
+    - fn: "*.kraken2.report_bracken.txt"
   rseqc/bam_stat:
     fn: "*.bam_stat.txt"
   rseqc/gene_body_coverage:
@@ -211,7 +211,7 @@ sp:
     skip: true
 
 fn_ignore_files:
-- "*umi_dedup.transcriptome.sorted.log"
+  - "*umi_dedup.transcriptome.sorted.log"
 
 # See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
 custom_data:
@@ -262,26 +262,26 @@ custom_data:
         description: User-provided strandedness
         cond_formatting_rules:
           blue:
-          - s_eq: "auto"
+            - s_eq: "auto"
           black:
-          - s_eq: "forward"
+            - s_eq: "forward"
           grey:
-          - s_eq: "reverse"
+            - s_eq: "reverse"
         cond_formatting_colours:
-        - grey: "#AAB7B8"
-        - black: "#17202A"
+          - grey: "#AAB7B8"
+          - black: "#17202A"
       Inferred strandedness:
         description: Interred strandedness
         cond_formatting_rules:
           blue:
-          - s_eq: "auto"
+            - s_eq: "auto"
           black:
-          - s_eq: "forward"
+            - s_eq: "forward"
           grey:
-          - s_eq: "reverse"
+            - s_eq: "reverse"
         cond_formatting_colours:
-        - grey: "#AAB7B8"
-        - black: "#17202A"
+          - grey: "#AAB7B8"
+          - black: "#17202A"
       Sense (%):
         max: 100
       Antisense (%):