Bump version for 3.3.0 release

.nf-core.yml

@@ -1,18 +1,19 @@
 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:
-  author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry"
+  author: "Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates,
+    Maxime Borry"
   description: Assembly, binning and annotation of metagenomes
   force: false
   is_nfcore: true
   name: mag
   org: nf-core
   outdir: .
-  version: 3.3.0dev
+  version: 3.3.0

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev [unreleased]
+## 3.3.0 [2024-12-16]
 
 ### `Added`
 

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.3.0"
+  target="_blank">nf-core/mag</a> analysis pipeline. For information about how to
+  interpret these results, please see the <a href="https://nf-co.re/mag/3.3.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
@@ -16,86 +17,98 @@ 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:
     file_format: "tsv"
     section_name: "Bowtie 2: host read removal"
-    description: "Reads are mapped against the host reference sequence. Only reads that do not align (concordantly) are kept for further analysis."
+    description: "Reads are mapped against the host reference sequence. Only reads
+      that do not align (concordantly) are kept for further analysis."
     plot_type: "bargraph"
     pconfig:
       id: "host_removal_bargraph"
@@ -118,53 +131,53 @@ 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"
 custom_logo_url: https://github.com/nf-core/mag/
 custom_logo_title: "nf-core/mag"
 
 ## Tool specific configuration
-prokka_fn_snames: True
+prokka_fn_snames: true
 
 ## General Stats customisation
 table_columns_visible:
   "FastQC: raw reads":
-    avg_sequence_length: True
+    avg_sequence_length: true
   "FastQC: after preprocessing":
-    avg_sequence_length: True
+    avg_sequence_length: true
   "fastp":
-    pct_duplication: False
-    after_filtering_q30_rate: False
-    after_filtering_q30_bases: False
+    pct_duplication: false
+    after_filtering_q30_rate: false
+    after_filtering_q30_bases: false
     filtering_result_passed_filter_reads: 3300
-    after_filtering_gc_content: False
-    pct_surviving: True
-    pct_adapter: True
-  "Kraken2": False
-  "Centrifuge": False
+    after_filtering_gc_content: false
+    pct_surviving: true
+    pct_adapter: true
+  "Kraken2": false
+  "Centrifuge": false
   "QUAST: assembly":
-    N75: True
-    L50: True
-    L75: True
-    "Largest contig": True
-    "Total length": True
-    N50: True
-  "Bowtie2: assembly": False
+    N75: true
+    L50: true
+    L75: true
+    "Largest contig": true
+    "Total length": true
+    N50: true
+  "Bowtie2: assembly": false
   "QUAST: bins":
-    N75: True
-    L50: True
-    L75: True
-    "Largest contig": True
-    "Total length": True
-    N50: True
-  "Prokka": False
+    N75: true
+    L50: true
+    L75: true
+    "Largest contig": true
+    "Total length": true
+    N50: true
+  "Prokka": false
 
 table_columns_placement:
   "FastQC: raw reads":
@@ -244,6 +257,6 @@ table_columns_name:
 custom_table_header_config:
   general_stats_table:
     "Total length":
-      hidden: True
+      hidden: true
     N50:
-      hidden: True
+      hidden: true