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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:
3-
- 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
7-
- params.lambda_reference
5+
- config_defaults:
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- params.phix_reference
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- params.lambda_reference
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nf_core_version: 3.2.1
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repository_type: pipeline
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template:

‎assets/multiqc_config.yml

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@@ -17,93 +17,93 @@ 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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- trimmomatic
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- fastqc
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- fastp
22+
- adapterremoval
23+
- custom_content
24+
- bowtie2
25+
- busco
26+
- quast
27+
- kraken
28+
- prokka
29+
- porechop
30+
- filtlong
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- trimmomatic
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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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- "trimmomatic"
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- "porechop"
43-
- "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
73-
sequences from microbial samples. The system uses a novel indexing scheme based
74-
on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
75-
Note: Figure title"
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extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
77-
format as Kraken. If activated, see the actual Kraken2 results in the section
78-
above."
79-
path_filters:
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- "*.centrifuge_kreport.txt"
81-
- "quast":
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name: "QUAST: assembly"
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info: "Assembly statistics of raw assemblies."
84-
path_filters:
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- "*rawassemblies.tsv"
86-
- "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"
99-
- "busco":
100-
info: "assesses genome assembly and annotation completeness with Benchmarking
101-
Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
102-
was used, only generic results for the selected domain are shown and only for
103-
genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
104-
i.e. not for contigs for which no BUSCO genes could be found. Bins for which
105-
a specific virus lineage was selected are also not shown."
106-
- "prokka"
35+
- "fastqc":
36+
name: "FastQC: raw reads"
37+
path_filters_exclude:
38+
- "*trimmed*"
39+
- "fastp"
40+
- "adapterremoval"
41+
- "trimmomatic"
42+
- "porechop"
43+
- "filtlong"
44+
- "fastqc":
45+
name: "FastQC: after preprocessing"
46+
info: "After trimming and, if requested, contamination removal."
47+
path_filters:
48+
- "*trimmed*"
49+
- "bowtie2":
50+
name: "Bowtie2: PhiX removal"
51+
info: "Mapping statistics of reads mapped against PhiX and subsequently removed."
52+
path_filters:
53+
- "*_phix_removed.bowtie2.log"
54+
- "bowtie2":
55+
name: "Bowtie2: host removal"
56+
info: "Mapping statistics of reads mapped against host genome and subsequently
57+
removed."
58+
path_filters:
59+
- "*_host_removed.bowtie2.log"
60+
- "kraken":
61+
name: "Kraken2"
62+
anchor: "Kraken2"
63+
target: "Kraken2"
64+
doi: "10.1101/gr.210641.116"
65+
path_filters:
66+
- "*.kraken2_report.txt"
67+
- "kraken":
68+
name: "Centrifuge"
69+
anchor: "centrifuge"
70+
target: "Centrifuge"
71+
doi: "10.1101/gr.210641.116"
72+
info: "is a very rapid and memory-efficient system for the classification of DNA
73+
sequences from microbial samples. The system uses a novel indexing scheme based
74+
on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
75+
Note: Figure title"
76+
extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
77+
format as Kraken. If activated, see the actual Kraken2 results in the section
78+
above."
79+
path_filters:
80+
- "*.centrifuge_kreport.txt"
81+
- "quast":
82+
name: "QUAST: assembly"
83+
info: "Assembly statistics of raw assemblies."
84+
path_filters:
85+
- "*rawassemblies.tsv"
86+
- "bowtie2":
87+
name: "Bowtie2: assembly"
88+
info: "Mapping statistics of reads mapped against assemblies."
89+
path_filters_exclude:
90+
- "*_host_removed.bowtie2.log"
91+
- "*_phix_removed.bowtie2.log"
92+
- "bcftools"
93+
- custom_content
94+
- "quast":
95+
name: "QUAST: bins"
96+
info: "Assembly statistics of binned assemblies."
97+
path_filters_exclude:
98+
- "*rawassemblies.tsv"
99+
- "busco":
100+
info: "assesses genome assembly and annotation completeness with Benchmarking
101+
Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection
102+
was used, only generic results for the selected domain are shown and only for
103+
genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull,
104+
i.e. not for contigs for which no BUSCO genes could be found. Bins for which
105+
a specific virus lineage was selected are also not shown."
106+
- "prokka"
107107

108108
custom_data:
109109
host_removal:
@@ -133,14 +133,14 @@ sp:
133133

134134
## File name cleaning
135135
extra_fn_clean_exts:
136-
- ".bowtie2"
137-
- "_ar2"
138-
- "host_removed"
139-
- "phix_removed"
140-
- "centrifuge_kreport"
141-
- "_fastp"
142-
- "_trimmomatic_trim.log"
143-
- "_trimmomatic_trim"
136+
- ".bowtie2"
137+
- "_ar2"
138+
- "host_removed"
139+
- "phix_removed"
140+
- "centrifuge_kreport"
141+
- "_fastp"
142+
- "_trimmomatic_trim.log"
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- "_trimmomatic_trim"
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## Prettification
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custom_logo: "mag_logo_mascot_light.png"

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