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[automated] Fix code linting
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‎.nf-core.yml‎

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@@ -1,10 +1,10 @@
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lint:
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files_unchanged:
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- lib/NfcoreTemplate.groovy
3+
- lib/NfcoreTemplate.groovy
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nextflow_config:
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- config_defaults:
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- params.phix_reference
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- params.lambda_reference
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- config_defaults:
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- params.phix_reference
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- params.lambda_reference
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nf_core_version: 3.2.0
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repository_type: pipeline
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template:

‎assets/multiqc_config.yml‎

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@@ -17,91 +17,91 @@ disable_version_detection: true
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data_format: "yaml"
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run_modules:
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- fastqc
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- fastp
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- adapterremoval
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- custom_content
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- bowtie2
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- busco
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- quast
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- kraken
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- prokka
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- porechop
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- filtlong
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- fastqc
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- fastp
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- adapterremoval
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- custom_content
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- bowtie2
25+
- busco
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- quast
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- kraken
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- prokka
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- porechop
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- filtlong
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## Module order
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top_modules:
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- "fastqc":
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name: "FastQC: raw reads"
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path_filters_exclude:
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- "*trimmed*"
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- "fastp"
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- "adapterremoval"
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- "porechop"
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- "filtlong"
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- "fastqc":
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name: "FastQC: after preprocessing"
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info: "After trimming and, if requested, contamination removal."
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path_filters:
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- "*trimmed*"
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- "bowtie2":
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name: "Bowtie2: PhiX removal"
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info: "Mapping statistics of reads mapped against PhiX and subsequently removed."
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path_filters:
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- "*_phix_removed.bowtie2.log"
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- "bowtie2":
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name: "Bowtie2: host removal"
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info: "Mapping statistics of reads mapped against host genome and subsequently
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removed."
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path_filters:
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- "*_host_removed.bowtie2.log"
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- "kraken":
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name: "Kraken2"
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anchor: "Kraken2"
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target: "Kraken2"
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doi: "10.1101/gr.210641.116"
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path_filters:
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- "*.kraken2_report.txt"
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- "kraken":
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name: "Centrifuge"
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anchor: "centrifuge"
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target: "Centrifuge"
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doi: "10.1101/gr.210641.116"
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info: "is a very rapid and memory-efficient system for the classification of DNA
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sequences from microbial samples. The system uses a novel indexing scheme based
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on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
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Note: Figure title"
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extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
75-
format as Kraken. If activated, see the actual Kraken2 results in the section
76-
above."
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path_filters:
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- "*.centrifuge_kreport.txt"
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- "quast":
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name: "QUAST: assembly"
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info: "Assembly statistics of raw assemblies."
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path_filters:
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- "*rawassemblies.tsv"
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- "bowtie2":
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name: "Bowtie2: assembly"
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info: "Mapping statistics of reads mapped against assemblies."
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path_filters_exclude:
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- "*_host_removed.bowtie2.log"
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- "*_phix_removed.bowtie2.log"
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- "bcftools"
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- custom_content
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- "quast":
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name: "QUAST: bins"
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info: "Assembly statistics of binned assemblies."
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path_filters_exclude:
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- "*rawassemblies.tsv"
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- "busco":
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info: "assesses genome assembly and annotation completeness with Benchmarking
99-
Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
100-
was used, only generic results for the selected domain are shown and only for
101-
genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
102-
i.e. not for contigs for which no BUSCO genes could be found. Bins for which
103-
a specific virus lineage was selected are also not shown."
104-
- "prokka"
34+
- "fastqc":
35+
name: "FastQC: raw reads"
36+
path_filters_exclude:
37+
- "*trimmed*"
38+
- "fastp"
39+
- "adapterremoval"
40+
- "porechop"
41+
- "filtlong"
42+
- "fastqc":
43+
name: "FastQC: after preprocessing"
44+
info: "After trimming and, if requested, contamination removal."
45+
path_filters:
46+
- "*trimmed*"
47+
- "bowtie2":
48+
name: "Bowtie2: PhiX removal"
49+
info: "Mapping statistics of reads mapped against PhiX and subsequently removed."
50+
path_filters:
51+
- "*_phix_removed.bowtie2.log"
52+
- "bowtie2":
53+
name: "Bowtie2: host removal"
54+
info: "Mapping statistics of reads mapped against host genome and subsequently
55+
removed."
56+
path_filters:
57+
- "*_host_removed.bowtie2.log"
58+
- "kraken":
59+
name: "Kraken2"
60+
anchor: "Kraken2"
61+
target: "Kraken2"
62+
doi: "10.1101/gr.210641.116"
63+
path_filters:
64+
- "*.kraken2_report.txt"
65+
- "kraken":
66+
name: "Centrifuge"
67+
anchor: "centrifuge"
68+
target: "Centrifuge"
69+
doi: "10.1101/gr.210641.116"
70+
info: "is a very rapid and memory-efficient system for the classification of DNA
71+
sequences from microbial samples. The system uses a novel indexing scheme based
72+
on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
73+
Note: Figure title"
74+
extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
75+
format as Kraken. If activated, see the actual Kraken2 results in the section
76+
above."
77+
path_filters:
78+
- "*.centrifuge_kreport.txt"
79+
- "quast":
80+
name: "QUAST: assembly"
81+
info: "Assembly statistics of raw assemblies."
82+
path_filters:
83+
- "*rawassemblies.tsv"
84+
- "bowtie2":
85+
name: "Bowtie2: assembly"
86+
info: "Mapping statistics of reads mapped against assemblies."
87+
path_filters_exclude:
88+
- "*_host_removed.bowtie2.log"
89+
- "*_phix_removed.bowtie2.log"
90+
- "bcftools"
91+
- custom_content
92+
- "quast":
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name: "QUAST: bins"
94+
info: "Assembly statistics of binned assemblies."
95+
path_filters_exclude:
96+
- "*rawassemblies.tsv"
97+
- "busco":
98+
info: "assesses genome assembly and annotation completeness with Benchmarking
99+
Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
100+
was used, only generic results for the selected domain are shown and only for
101+
genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
102+
i.e. not for contigs for which no BUSCO genes could be found. Bins for which
103+
a specific virus lineage was selected are also not shown."
104+
- "prokka"
105105

106106
custom_data:
107107
host_removal:
@@ -131,12 +131,12 @@ sp:
131131

132132
## File name cleaning
133133
extra_fn_clean_exts:
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- ".bowtie2"
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- "_ar2"
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- "host_removed"
137-
- "phix_removed"
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- "centrifuge_kreport"
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- "_fastp"
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- ".bowtie2"
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- "_ar2"
136+
- "host_removed"
137+
- "phix_removed"
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- "centrifuge_kreport"
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- "_fastp"
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## Prettification
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custom_logo: "mag_logo_mascot_light.png"

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