nf-core · KateSakharova · May 6, 2026 · Apr 24, 2026 · Apr 24, 2026 · Apr 27, 2026
diff --git a/assets/multiqc_config.yml b/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"
diff --git a/conf/modules.config b/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,

diff --git a/docs/output.md b/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

diff --git a/main.nf b/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
     }

diff --git a/modules/local/ena_webin_cli_download/environment.yml b/modules/local/ena_webin_cli_download/environment.yml
diff --git a/modules/local/ena_webin_cli_download/main.nf b/modules/local/ena_webin_cli_download/main.nf
diff --git a/modules/local/ena_webin_cli_download/meta.yml b/modules/local/ena_webin_cli_download/meta.yml
diff --git a/modules/local/ena_webin_cli_download/tests/main.nf.test b/modules/local/ena_webin_cli_download/tests/main.nf.test
diff --git a/modules/local/ena_webin_cli_download/tests/main.nf.test.snap b/modules/local/ena_webin_cli_download/tests/main.nf.test.snap
diff --git a/modules/local/ena_webin_cli_wrapper/main.nf b/modules/local/ena_webin_cli_wrapper/main.nf
@@ -5,12 +5,12 @@ process ENA_WEBIN_CLI_WRAPPER {
 
     label 'process_low'
     tag "${meta.id}"
-    container "quay.io/microbiome-informatics/java_mgnify-pipelines-toolkit:1.4.21"
+    // ena-webin-cli 9.0.3 + mgnify-pipelines-toolkit 1.4.24
+    container "community.wave.seqera.io/library/ena-webin-cli_mgnify-pipelines-toolkit:0fd318932c5ba88e"
     stageInMode 'copy'
 
     input:
     tuple val(meta), path(submission_item), path(manifest)
-    path(webin_cli_jar)
     val test_upload
     val webincli_mode
 
@@ -22,17 +22,14 @@ process ENA_WEBIN_CLI_WRAPPER {
     def args               = task.ext.args   ?: ""
     def prefix             = task.ext.prefix ?: "${meta.id}"
     def test_flag          = test_upload     ? "--test" : ""
+    def fasta_dir          = submission_item.toRealPath().parent
 
     """
-    # change FASTA path in manifest to current workdir
-    export ITEM_FULL_PATH=\$(readlink -f ${submission_item})
-    sed 's|^FASTA\t.*|FASTA\t'"\${ITEM_FULL_PATH}"'|g' ${manifest} > ${prefix}_updated_manifest.manifest
-
     webin_cli_handler \\
-      -m ${prefix}_updated_manifest.manifest \\
+      -m ${manifest} \\
       -o ${prefix}_accessions.tsv \\
-      --webin-cli-jar ${webin_cli_jar} \\
       --mode ${webincli_mode} \\
+      --fasta-dir ${fasta_dir} \\
       ${test_flag} \\
       ${args}
 

diff --git a/modules/local/ena_webin_cli_wrapper/meta.yml b/modules/local/ena_webin_cli_wrapper/meta.yml
@@ -27,11 +27,6 @@ input:
         type: file
         description: |
           Webin-CLI submission manifest file.
-  - - webin_cli_jar:
-        type: file
-        description: |
-          The Webin-CLI JAR file downloaded by ena_webin_cli_download.
-        pattern: "webin-cli-*.jar"
   - - test_upload:
         type: value
         description: Whether to run ENA Webin-CLI in test mode.