added meta

assets/methods_description_template.yml

@@ -0,0 +1,35 @@
+id: "ebi-metagenomics/emg-viral-pipeline-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "ebi-metagenomics/emg-viral-pipeline Methods Description"
+section_href: "https://github.com/EBI-Metagenomics/emg-viral-pipeline"
+plot_type: "html"
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using ebi-metagenomics/genomes-generation v${workflow.manifest.version} (${doi_text}; <a href="https://doi.org/10.1093/nargab/lqac007">Krakau <em>et al.</em>, 2022</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
+  <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
+  <h4>References</h4>
+  <ul>
+    <li>
+      Informative Regions In Viral Genomes
+      <i>Viruses (2021)</i>
+      doi: <a href="https://doi.org/10.3390/v13061164">10.3390/v13061164</a>
+      Moreno-Gallego, Jaime Leonardo, and Alejandro Reyes
+    </li>
+    <li>
+      VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
+      <i>bioRxiv</i>
+      doi: <a href="https://doi.org/10.1101/2022.08.22.504484">10.1101/2022.08.22.504484</a>
+      Rangel-Pineros, Guillermo, et al.
+    </li>
+    ${tool_bibliography}
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>

assets/multiqc_config.yml

@@ -0,0 +1,61 @@
+report_comment: >
+
+  This report has been generated by the <a href="https://github.com/ebi-metagenomics/emg-viral-pipeline/" target="_blank">ebi-metagenomics/emg-viral-pipeline</a> pipeline.
+
+report_section_order:
+  "ebi-metagenomics/emg-viral-pipeline-methods-description":
+    order: -1000
+  software_versions:
+    order: -1001
+  "ebi-metagenomics/emg-viral-pipeline-summary":
+    order: -1002
+
+export_plots: true
+
+data_format: "yaml"
+
+run_modules:
+  - fastqc
+  - fastp
+
+## Module order
+module_order:
+  - fastqc
+  - fastp
+
+## File name cleaning
+extra_fn_clean_exts:
+  - "_fastp"
+
+## Prettification
+custom_logo: "mgnify_logo.png"
+custom_logo_url: https://github.com/ebi-metagenomics/emg-viral-pipeline/
+custom_logo_title: "ebi-metagenomics/emg-viral-pipeline"
+
+## General Stats customisation
+table_columns_visible:
+  "fastp":
+    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
+
+table_columns_placement:
+  "fastp":
+    pct_duplication: 3000
+    after_filtering_q30_rate: 3100
+    after_filtering_q30_bases: 3200
+    filtering_result_passed_filter_reads: 3300
+    after_filtering_gc_content: 3400
+    pct_surviving: 3500
+    pct_adapter: 3600
+
+custom_table_header_config:
+  general_stats_table:
+    "Total length":
+      hidden: True
+    N50:
+      hidden: True

configs/conda.config

@@ -1,24 +1,20 @@
 process {
-    withLabel: annotation {         conda = "$baseDir/envs/python3.yaml" }
-    withLabel: assign {             conda = "$baseDir/envs/python3.yaml" }
-    withLabel: balloon {            conda = "$baseDir/envs/balloon.yaml" }
-    withLabel: basics {             conda = "$baseDir/envs/python3.yaml" }
-    withLabel: blast {              conda = "$baseDir/envs/blast.yaml" }
-    withLabel: fastp {              conda = "$baseDir/envs/fastp.yaml" } 
-    withLabel: fastqc {             conda = "$baseDir/envs/fastqc.yaml" }
-    withLabel: hmmscan {            conda = "$baseDir/envs/hmmer.yaml" }
-    withLabel: kaiju {              conda = "$baseDir/envs/kaiju.yaml" }
-    withLabel: krona {              conda = "$baseDir/envs/krona.yaml"  }
-    withLabel: plot_contig_map {    conda = "$baseDir/envs/r.yaml" }
-    withLabel: multiqc {            conda = "$baseDir/envs/multiqc.yaml" }
-    withLabel: parse {              conda = "$baseDir/envs/python3.yaml" }
-    withLabel: prodigal {           conda = "$baseDir/envs/prodigal.yaml" }
-    withLabel: phanotate {          conda = "$baseDir/envs/phanotate.yaml" }
-    withLabel: python3 {            conda = "$baseDir/envs/python3.yaml" }
-    withLabel: ratio_evalue {       conda = "$baseDir/envs/python3.yaml" }
-    withLabel: ruby {               conda = "$baseDir/envs/ruby.yaml" } 
-    withLabel: spades {             conda = "$baseDir/envs/spades.yaml" } 
-	withLabel: virsorter {          conda = "$baseDir/envs/virsorter.yaml" }
-    withLabel: virfinder {          conda = "$baseDir/envs/virfinder.yaml" }
-    withLabel: checkV {             conda = "$baseDir/envs/checkv.yaml" }
+    withNAME: ANNOTATION {         conda = "$baseDir/envs/python3.yaml" }
+    withNAME: ASSIGN {             conda = "$baseDir/envs/python3.yaml" }
+    withNAME: BALLOON {            conda = "$baseDir/envs/balloon.yaml" }
+    withNAME: basics {             conda = "$baseDir/envs/python3.yaml" }
+    withNAME: BLAST {              conda = "$baseDir/envs/blast.yaml" }
+    withNAME: HMMSCAN {            conda = "$baseDir/envs/hmmer.yaml" }
+    withNAME: KAIJU {              conda = "$baseDir/envs/kaiju.yaml" }
+    withNAME: KRONA {              conda = "$baseDir/envs/krona.yaml"  }
+    withNAME: PLOT_CONTIG_MAP {    conda = "$baseDir/envs/r.yaml" }
+    withNAME: PARSE {              conda = "$baseDir/envs/python3.yaml" }
+    withNAME: PRODIGAL {           conda = "$baseDir/envs/prodigal.yaml" }
+    withNAME: PHANOTATE {          conda = "$baseDir/envs/phanotate.yaml" }
+    withNAME: python3 {            conda = "$baseDir/envs/python3.yaml" }
+    withNAME: RATIO_EVALUE {       conda = "$baseDir/envs/python3.yaml" }
+    withNAME: ruby {               conda = "$baseDir/envs/ruby.yaml" } 
+	withNAME: VIRSORTER {          conda = "$baseDir/envs/virsorter.yaml" }
+    withNAME: VIRFINDER {          conda = "$baseDir/envs/virfinder.yaml" }
+    withNAME: CHECKV {             conda = "$baseDir/envs/checkv.yaml" }
 }