Edit multiQC report

assets/multiqc_config.yml

@@ -11,5 +11,156 @@ report_section_order:
     order: -1002
 
 export_plots: true
-
+disable_general_stats: true
 disable_version_detection: true
+
+custom_content:
+  order:
+    - assembly_metadata
+    - genome_metadata
+    - sample_registration
+    - submission_results_assemblies
+    - submission_results_genomes
+
+sp:
+  assembly_metadata:
+    fn_re: ".*assemblies_metadata.csv$"
+  genome_metadata:
+    fn_re: ".*genomes_metadata.tsv$"
+  sample_registration:
+    fn_re: '.*registered.*\.tsv$'
+  submission_results_genomes:
+    fn_re: 'genomes_accessions\.tsv$'
+  submission_results_assemblies:
+    fn_re: 'assemblies_accessions\.tsv$'
+
+# Custom data configuration
+custom_data:
+  assembly_metadata:
+    id: "assembly_metadata"
+    section_name: "Assembly metadata"
+    description: "Metadata for submitted assemblies"
+    file_format: "csv"
+    plot_type: "table"
+    pconfig:
+      id: "assembly_metadata"
+      title: "Assembly metadata table"
+    headers:
+      runs:
+        title: "Runs"
+      assembly_coverage:
+        title: "Coverage"
+      assembler:
+        title: "Assembler"
+      assembler_version:
+        title: "Version"
+      file_path:
+        title: "Filepath"
+      sample: "Sample"
+
+  genome_metadata:
+    id: "genome_metadata"
+    section_name: "Genome metadata"
+    description: "Metadata for submitted genomes"
+    file_format: "tsv"
+    plot_type: "table"
+    pconfig:
+      id: "genome_metadata"
+      title: "Genome metadata table"
+    headers:
+      genome_name:
+        title: "Genome name"
+      genome_path:
+        title: "Genome path"
+      accessions:
+        title: "Accession"
+      assembly_software:
+        title: "Assembly software"
+      binning_software:
+        title: "Binning software"
+      binning_parameters:
+        title: "Binning parameters"
+      stats_generation_software:
+        title: "Stats software"
+      completeness:
+        title: "Completeness (%)"
+      contamination:
+        title: "Contamination (%)"
+      genome_coverage:
+        title: "Coverage"
+      metagenome:
+        title: "Metagenome"
+      co-assembly:
+        title: "Co-assembly"
+      broad_environment:
+        title: "Broad environment"
+      local_environment:
+        title: "Local environment"
+      environmental_medium:
+        title: "Environmental medium"
+      rRNA_presence:
+        title: "rRNA presence"
+      NCBI_lineage:
+        title: "NCBI lineage"
+
+  sample_registration:
+    file_format: "tsv"
+    plot_type: "table"
+    pconfig:
+      id: "sample_registration"
+      title: "Sample registration assigned accessions"
+    headers:
+      alias:
+        title: "ID"
+        description: "FASTA file for upload"
+      accession:
+        title: "ENA sample accession"
+        description: "Assigned accession after submission"
+
+  submission_results_assemblies:
+    id: "submission_results_assemblies"
+    section_name: "Submission results"
+    description: >
+      Accessions assigned during upload process.
+      As all assemblies in ENA are submitted as ‘analyses’, for each assembly submission, Webin will report a unique accession number that starts with ERZ.
+      For most assemblies, this accession number is for internal processing only and will not be visible in the browser.
+      As a result, for most assemblies you will receive additional post-processing accession numbers starting with GCA_.
+      Always make a note of any accessions you receive as these are the unique identifiers for each of your submissions to ENA.
+      The ERZ accession can be used to access information on the progress of the internal processing of each assembly through the [Webin Portal](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/submissions-portal.html).
+      You can also use this service to see the assigned chromosome, contig, and scaffold accessions.
+      Please follow the Webin Portal link to learn more about this.
+      See individual submission guidelines for information on what accessions you will receive for each assembly type.
+      More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions.
+    file_format: "tsv"
+    plot_type: "table"
+    pconfig:
+      id: "Assemblies assigned accessions"
+      title: "Submission results"
+      col1_header: "ID"
+      col2_header: "ENA accession"
+    headers:
+      alias:
+        title: "ID"
+        description: "FASTA file for upload"
+      accession:
+        title: "ENA accession"
+        description: "Assigned accession after submission"
+
+  submission_results_genomes:
+    id: "submission_results_genomes"
+    section_name: "Submission results"
+    description: "Accessions assigned during upload process."
+    file_format: "tsv"
+    plot_type: "table"
+    pconfig:
+      id: "Genomes assigned accessions"
+      title: "Submission results"
+      col1_header: "ID"
+      col2_header: "ENA accession"
+    headers:
+      alias:
+        title: "ID"
+        description: "FASTA file for upload"
+      accession:
+        title: "ENA accession"
+        description: "Assigned accession after submission"

conf/modules.config

@@ -187,7 +187,12 @@ process {
     //
 
     withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        ext.args   = {
+            [
+                params.multiqc_title ? "--title \"$params.multiqc_title\"" : '',
+                "-p"
+            ].findAll().join(' ')
+        }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,

docs/output.md

@@ -50,6 +50,12 @@ When `--mode metagenomic_assemblies` is used, results are written under `metagen
 
 Assembly study registration, manifest generation, and Webin-CLI submission are executed by the workflow, but their intermediate outputs are not currently published into `--outdir` by the pipeline.
 
+> [!NOTE]
+> As all assemblies in ENA are submitted as ‘analyses’, for each assembly submission, Webin will report a unique accession number that starts with ERZ.
+> For most assemblies, this accession number is for **internal processing only** and will not be visible in the browser.
+> As a result, for most assemblies you will receive additional post-processing accession numbers starting with GCA\_.
+> More information about accessions can be found in ENA docs: https://ena-docs.readthedocs.io/en/latest/submit/assembly.html#accessions.'
+
 ## Common outputs
 
 ### MultiQC

main.nf

@@ -55,7 +55,8 @@ workflow NFCORE_SEQSUBMIT {
             params.upload_tpa,
             params.test_upload,
             params.webin_cli_version,
-            params.webincli_mode
+            params.webincli_mode,
+            params.outdir
         )
         ch_multiqc_report = GENOMESUBMIT.out.multiqc_report
     } else if (params.mode == "metagenomic_assemblies") {
@@ -66,7 +67,8 @@ workflow NFCORE_SEQSUBMIT {
             params.upload_tpa,
             params.test_upload,
             params.webin_cli_version,
-            params.webincli_mode
+            params.webincli_mode,
+            params.outdir
         )
         ch_multiqc_report = ASSEMBLYSUBMIT.out.multiqc_report
     }

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:

subworkflows/local/utils_nfcore_seqsubmit_pipeline/main.nf

@@ -183,24 +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
+
+    def mgnify_tools = [
+        params.mode == "metagenomic_assemblies" ? "Manifests for metagenomic assemblies upload were created by assembly_uploader (Richardson et al. 2023)." : "",
+        params.mode != "metagenomic_assemblies" ? "Samples registration and upload manifests generation for bins/MAGs were done by genome_uploader (Gurbich et al. 2023).": ""
+    ].join(' ').trim()
+
+    def ena_tools = [
+        "Submission to ENA was done by webin-cli (David, Yuan, et al. 2025)."
+    ].join(' ').trim()
+
+    def preprocessing_tools = [
+        "Input FASTA validation was done by py_fasta_validator (Edwards et al. 2023)."
+    ].join(' ').trim()
+
+    def stats_tools = [
+        params.mode != "metagenomic_assemblies" ? "Completeness and contamination metrics was performed by CheckM2 (Chklovski et al. 2023)." : "",
+        "Coverage calculation for metagenomic assemblies/bins/MAGs was done by CoverM (Aroney et el. 2025)."
+    ].join(' ').trim()
+
+    def taxonomy_tools = [
+        params.mode != "metagenomic_assemblies" ? "Taxonomy was assigned by CAT_pack (Von Meijenfeldt et al. 2019)." : ""
+    ].join(' ').trim()
+
+    def rna_tools = [
+        params.mode != "metagenomic_assemblies" ? "Bacterial ribosomal RNA prediction was performed by barrnap (Seemann T. 2013)." : "",
+        params.mode != "metagenomic_assemblies" ? "Transfer RNA genes were detected by 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)",
-            "."
+            preprocessing_tools,
+            stats_tools,
+            taxonomy_tools,
+            rna_tools,
+            mgnify_tools,
+            ena_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>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>"
+            '<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: <a href="https://doi.org/10.1093/nar/gkac1080"10.1093/nar/gkac1080</a></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: <a href="https://doi.org/10.1016/j.jmb.2023.168016"10.1016/j.jmb.2023.168016</a></li>',
+            '<li>webin-cli: David, Y., Alisha, A., Awais, A., Rajkumar, D., Dipayan, G., Muhammad, H., ... & Ugis, S. (2026). The European Nucleotide Archive in 2025. Nucleic Acids Research, 54(D1), D120-D127. doi: <a href="https://doi.org/10.1093/nar/gkaf1295"10.1093/nar/gkaf1295</a></li>',
+            '<li>Edwards, R. (2023). linsalrob/py_fasta_validator: Compressy. doi: <a href="https://doi.org/10.5281/zenodo.5002710"10.5281/zenodo.5002710</a></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: <a href="https://doi.org/10.1038/s41592-023-01940-w"10.1038/s41592-023-01940-w</a></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: <a href="https://doi.org/10.1093/bioinformatics/btaf147"10.1093/bioinformatics/btaf147</a></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: <a href="https://doi.org/10.1038/s41467-024-47155-1"10.1038/s41467-024-47155-1</a></li>',
+            '<li>barrnap: Seemann, T. (2014). barrnap: Bacterial ribosomal RNA predictor. barrnap: Bacterial ribosomal RNA predictor. <a href="http://vicbioinformatics.com/"vicbioinformatics.com</a></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: <a href="https://doi.org/10.1093/nar/gkab688"10.1093/nar/gkab688</a></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: <a href="https://doi.org/10.1093/bioinformatics/btw354"10.1093/bioinformatics/btw354</a></li>'
         ].join(' ').trim()
 
     return reference_text
@@ -230,9 +271,8 @@ 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/assemblysubmit.nf

@@ -37,6 +37,7 @@ workflow ASSEMBLYSUBMIT {
     test_upload          // val: true for test upload mode
     webin_cli_version    // val: WebinCLI tool version to download and use for submission
     webincli_mode        // val: either 'validate' or 'submit' to specify WebinCLI mode of operation
+    outdir
 
     main:
     ch_versions = channel.empty()
@@ -195,13 +196,31 @@ workflow ASSEMBLYSUBMIT {
     //
     // Collate and save software versions
     //
-    softwareVersionsToYAML(ch_versions)
+    def topic_versions = channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+        }
+        .groupTuple(by:0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+        .mix(topic_versions_string)
         .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
+            storeDir: "${outdir}/pipeline_info",
             name: 'nf_core_'  +  'seqsubmit_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
-        ).set { ch_collated_versions }
+        )
 
 
     //
@@ -227,6 +246,8 @@ workflow ASSEMBLYSUBMIT {
     ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
+    ch_multiqc_files = ch_multiqc_files.mix(CONCAT_ACCESSIONS.out.file_out)
+    ch_multiqc_files = ch_multiqc_files.mix(CREATE_ASSEMBLY_METADATA_CSV.out.csv)
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(