add citations

assets/multiqc_config.yml

@@ -13,3 +13,50 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
+
+custom_content:
+  order:
+    - sample_registration
+    - submission_results
+
+# Custom data configuration
+custom_data:
+
+  sample_registration:
+    id: 'sample_registration'
+    section_name: 'genpmes_samples'
+    description: 'Sample assigned during registration process'
+    file_format: 'tsv'
+    plot_type: 'table'
+    pconfig:
+      id: 'sample_registration'
+      title: 'Sample registration assigned accessions'
+      col1_header: 'ID'
+      col2_header: 'ENA sample accession'
+    headers:
+      alias:
+        title: 'Uploaded fasta'
+        description: 'FASTA file for upload'
+      accession:
+        title: 'ENA sample accession'
+        description: 'Assigned sample accession after registration'
+
+  submission_results:
+    id: 'submission_results'
+    section_name: 'Submission results'
+    description: 'Accessions assigned during upload process'
+    file_format: 'tsv'
+    plot_type: 'table'
+    pconfig:
+      id: 'custom_metrics_table'
+      title: 'Submission results'
+      col1_header: 'ID'
+      col2_header: 'ENA accession'
+    headers:
+      alias:
+        title: 'Uploaded fasta'
+        description: 'FASTA file for upload'
+      accession:
+        title: 'ENA accession'
+        description: 'Assigned accession after submission'
+

modules/local/ena_webin_cli_wrapper/main.nf

@@ -5,7 +5,7 @@ process ENA_WEBIN_CLI_WRAPPER {
 
     label 'process_low'
     tag "${meta.id}"
-    container "quay.io/microbiome-informatics/java_mgnify-pipelines-toolkit:1.4.21"
+    container "community.wave.seqera.io/library/ena-webin-cli_mgnify-pipelines-toolkit:0fd318932c5ba88e"
     stageInMode 'copy'
 
     input:
@@ -14,6 +14,7 @@ process ENA_WEBIN_CLI_WRAPPER {
 
     output:
     tuple val(meta), path("*_accessions.tsv"),  emit: accessions
+    path("*_accessions_mqc.tsv"),               emit: accessions_multiqc
     path "versions.yml",                        emit: versions
 
     script:
@@ -35,6 +36,8 @@ process ENA_WEBIN_CLI_WRAPPER {
       ${test_flag} \\
       ${args}
 
+    cp ${prefix}_accessions.tsv ${prefix}_accessions_mqc.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version 2>&1 | sed 's/Python //g')

subworkflows/local/utils_nfcore_seqsubmit_pipeline/main.nf

@@ -183,23 +183,65 @@ def validateInputSamplesheet(input) {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
+    // fastafalidator
+
+    def mgnify_tools = [
+        "assembly_uploader (Richardson et al. 2023)",
+        "genome_uploader (Gurbich et al. 2023)"
+    ].join(' ').trim()
+
+    def ena_tools = [
+        "webin-cli (European Nucleotide Archive)"
+    ].join(' ').trim()
+
+    def preprocessing_tools = [
+        "py_fasta_validator (Edwards et al. 2023)"
+    ].join(' ').trim()
+
+    def stats_tools = [
+        "CheckM2 (Chklovski et al. 2023)",
+        "CoverM (Aroney et el. 2025)"
+    ].join(' ').trim()
+
+    def taxonomy_tools = [
+        "CAT_pack (Von Meijenfeldt et al. 2019)"
+    ].join(' ').trim()
+
+    def rna_tools = [
+        "barrnap (Author: Torsten Seemann)",
+        "tRNAscan-SE (Chan et al. 2021)"
+    ].join(' ').trim()
+
+    def postprocessing_text = "MultiQC (Ewels et al. 2016)"
+
     def citation_text = [
-            "Tools used in the workflow included:",
-            "MultiQC (Ewels et al. 2016)",
-            "."
+            mgnify_tools,
+            ena_tools,
+            preprocessing_tools,
+            stats_tools,
+            taxonomy_tools,
+            rna_tools,
+            postprocessing_text
         ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
+            "<li>Richardson, L., Allen, B., Baldi, G., Beracochea, M., Bileschi, M. L., Burdett, T., ... & Finn, R. D. (2023). MGnify: the microbiome sequence data analysis resource in 2023. Nucleic acids research, 51(D1), D753-D759. doi: /10.1093/nar/gkac1080</li>",
+            "<li>Gurbich, T. A., Almeida, A., Beracochea, M., Burdett, T., Burgin, J., Cochrane, G., ... & Finn, R. D. (2023). MGnify genomes: a resource for biome-specific microbial genome catalogues. Journal of molecular biology, 435(14), 168016. doi: /10.1016/j.jmb.2023.168016</li>",
+            "<li>webin-cli: GitHub: https://github.com/enasequence/webin-cli. Docs: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html</li>",
+            "<li>Edwards, R. (2023). linsalrob/py_fasta_validator: Compressy. doi: /10.5281/zenodo.5002710</li>",
+            "<li>Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: 10.1038/s41592-023-01940-w</li>",
+            "<li>Aroney, S. T., Newell, R. J., Nissen, J. N., Camargo, A. P., Tyson, G. W., & Woodcroft, B. J. (2025). CoverM: read alignment statistics for metagenomics. Bioinformatics, 41(4), btaf147. doi: /10.1093/bioinformatics/btaf147</li>",
+            "<li>Von Meijenfeldt, F. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome biology, 20(1), 217. doi: /10.1038/s41467-024-47155-1</li>",
+            "<li>barrnap: GitHub: https://github.com/tseemann/barrnap</li>",
+            "<li>Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021). tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic acids research, 49(16), 9077-9096. doi: /10.1093/nar/gkab688</li>",
             "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
         ].join(' ').trim()
 
@@ -230,9 +272,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["tool_citations"] = ""
     meta["tool_bibliography"] = ""
 
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    // meta["tool_bibliography"] = toolBibliographyText()
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text

workflows/genomesubmit.nf

@@ -352,6 +352,13 @@ workflow GENOMESUBMIT {
     ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
+    samples_mqc = CREATE_MANIFESTS.out.upload_registered_mags
+        .map { meta, file ->
+            def newFile = file.copyTo(file.parent.resolve("${file.baseName}_mqc.tsv"))
+            return newFile
+        }
+    ch_multiqc_files = ch_multiqc_files.mix(samples_mqc)
+    ch_multiqc_files = ch_multiqc_files.mix(SUBMIT.out.accessions_multiqc)
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(