correct the format

nf-core · Dec 19, 2024 · a81eed0 · a81eed0
1 parent 9b0e463
commit a81eed0
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diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -61,23 +61,23 @@ custom_logo_url: https://nf-co.re/taxprofiler
 custom_logo_title: "nf-core/taxprofiler"
 
 run_modules:
-- fastqc
-- adapterremoval
-- fastp
-- nonpareil
-- bbduk
-- prinseqplusplus
-- porechop
-- filtlong
-- nanoq
-- bowtie2
-- samtools
-- kraken
-- kaiju
-- diamond
-- malt
-- motus
-- custom_content
+  - fastqc
+  - adapterremoval
+  - fastp
+  - nonpareil
+  - bbduk
+  - prinseqplusplus
+  - porechop
+  - filtlong
+  - nanoq
+  - bowtie2
+  - samtools
+  - kraken
+  - kaiju
+  - diamond
+  - malt
+  - motus
+  - custom_content
 
 sp:
   diamond:
@@ -93,81 +93,81 @@ sp:
     contents_re: " "
 
 top_modules:
-- "fastqc":
-    name: "FastQC / Falco (pre-Trimming)"
-    path_filters:
-    - "*raw*"
-    path_filters_exclude:
-    - "*processed*"
-    extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
-      the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
-- "fastqc":
-    name: "FastQC / Falco (post-Trimming)"
-    path_filters:
-    - "*processed*"
-    path_filters_exclude:
-    - "*raw*"
-    extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
-      the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
-- nonpareil
-- "porechop":
-    name: "Porechop"
-    anchor: "porechop"
-    target: "Porechop"
-    path_filters:
-    - "*porechop.log"
-    extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
-      this means that porechop did not detect any adapters and therefore no statistics
-      generated."
-- "porechop":
-    name: "Porechop_ABI"
-    anchor: "porechop_abi"
-    target: "Porechop_ABI"
-    doi: "10.1093/bioadv/vbac085"
-    info: "find and remove adapters from Oxford Nanopore reads."
-    path_filters:
-    - "*porechop_abi.log"
-    extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
-      this means that porechop_abi did not detect any adapters and therefore no statistics
-      generated."
-- "bowtie2":
-    name: "bowtie2"
-- "samtools":
-    name: "Samtools Stats"
-- "kraken":
-    name: "Kraken"
-    path_filters:
-    - "*.kraken2.kraken2.report.txt"
-- "kraken":
-    name: "Bracken"
-    anchor: "bracken"
-    target: "Bracken"
-    doi: "10.7717/peerj-cs.104"
-    info: "Estimates species abundances in metagenomics samples by probabilistically
-      re-distributing reads in the taxonomic tree."
-    extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing
-      the same output format as Kraken. Abundance information is currently not supported
-      in MultiQC."
-    path_filters:
-    - "*.bracken.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.txt"
-- "malt":
-    name: "MALT"
-- "kaiju":
-    name: "Kaiju"
+  - "fastqc":
+      name: "FastQC / Falco (pre-Trimming)"
+      path_filters:
+        - "*raw*"
+      path_filters_exclude:
+        - "*processed*"
+      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
+        the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+  - "fastqc":
+      name: "FastQC / Falco (post-Trimming)"
+      path_filters:
+        - "*processed*"
+      path_filters_exclude:
+        - "*raw*"
+      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
+        the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+  - nonpareil
+  - "porechop":
+      name: "Porechop"
+      anchor: "porechop"
+      target: "Porechop"
+      path_filters:
+        - "*porechop.log"
+      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
+        this means that porechop did not detect any adapters and therefore no statistics
+        generated."
+  - "porechop":
+      name: "Porechop_ABI"
+      anchor: "porechop_abi"
+      target: "Porechop_ABI"
+      doi: "10.1093/bioadv/vbac085"
+      info: "find and remove adapters from Oxford Nanopore reads."
+      path_filters:
+        - "*porechop_abi.log"
+      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
+        this means that porechop_abi did not detect any adapters and therefore no statistics
+        generated."
+  - "bowtie2":
+      name: "bowtie2"
+  - "samtools":
+      name: "Samtools Stats"
+  - "kraken":
+      name: "Kraken"
+      path_filters:
+        - "*.kraken2.kraken2.report.txt"
+  - "kraken":
+      name: "Bracken"
+      anchor: "bracken"
+      target: "Bracken"
+      doi: "10.7717/peerj-cs.104"
+      info: "Estimates species abundances in metagenomics samples by probabilistically
+        re-distributing reads in the taxonomic tree."
+      extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing
+        the same output format as Kraken. Abundance information is currently not supported
+        in MultiQC."
+      path_filters:
+        - "*.bracken.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.txt"
+  - "malt":
+      name: "MALT"
+  - "kaiju":
+      name: "Kaiju"
 
 # It is not possible to set placement for custom kraken
 # and centrifuge columns.
@@ -374,18 +374,18 @@ table_columns_name:
     reads_mapped_percent: "% Mapped Reads"
 
 extra_fn_clean_exts:
-- "kraken2.report.txt"
-- ".txt"
-- ".settings"
-- ".bbduk"
-- ".unmapped"
-- "_filtered"
-- "porechop"
-- "porechop_abi"
-- "_processed"
-- ".diamond"
-- type: remove
-  pattern: "_falco"
+  - "kraken2.report.txt"
+  - ".txt"
+  - ".settings"
+  - ".bbduk"
+  - ".unmapped"
+  - "_filtered"
+  - "porechop"
+  - "porechop_abi"
+  - "_processed"
+  - ".diamond"
+  - type: remove
+    pattern: "_falco"
 
 section_comments:
   general_stats: "By default, all read count columns are displayed as millions (M)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -124,11 +124,7 @@
         },
         {
             "@id": "main.nf",
-            "@type": [
-                "File",
-                "SoftwareSourceCode",
-                "ComputationalWorkflow"
-            ],
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "creator": [
                 {
                     "@id": "#jfy133@gmail.com"
@@ -161,9 +157,7 @@
                 "taxonomic-classification",
                 "taxonomic-profiling"
             ],
-            "license": [
-                "MIT"
-            ],
+            "license": ["MIT"],
             "maintainer": [
                 {
                     "@id": "#jfy133@gmail.com"
@@ -175,22 +169,15 @@
                     "@id": "https://orcid.org/0009-0006-0893-3771"
                 }
             ],
-            "name": [
-                "nf-core/taxprofiler"
-            ],
+            "name": ["nf-core/taxprofiler"],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": [
-                "https://github.com/nf-core/taxprofiler",
-                "https://nf-co.re/taxprofiler/1.2.2/"
-            ],
-            "version": [
-                "1.2.2"
-            ]
+            "url": ["https://github.com/nf-core/taxprofiler", "https://nf-co.re/taxprofiler/1.2.2/"],
+            "version": ["1.2.2"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -370,4 +357,4 @@
             "name": "Sofia Stamouli"
         }
     ]
-}
+}