KateSakharova · Oct 19, 2026 · Oct 15, 2026 · Oct 15, 2026 · Oct 14, 2026 · Oct 15, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,32 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1dev - [date]
+
+### `Fixed`
+
+- [#106](https://github.com/nf-core/seqsubmit/pull/106)
+  - Added support for metatranscriptome submission for ASSEMBLYSUBMIT
+  - Set retry to assembly_uploader
+- [#108](https://github.com/nf-core/seqsubmit/pull/108)
+  - Added test usecase in test-datasets https://github.com/nf-core/test-datasets/pull/2324 with contamination=0
+- [#107](https://github.com/nf-core/seqsubmit/pull/107)
+  - Fix `GENOMESUBMIT` treating a zero-valued completeness/contamination as a missing one. The branch that decides whether to (re)compute the statistics with CheckM2 tested the samplesheet values for Groovy truthiness, and the number `0` is falsey
+
+    ```groovy
+    genome_evaluation_input: !(meta.completeness) || !(meta.contamination) || !(meta.stats_generation_software)
+    ```
+
+    A genome with a legitimate value of `0` — a clean bin with 0% contamination — was therefore sent to `GENOME_EVALUATION`, where the supplied values were silently replaced by the recomputed ones. `stats_generation_software` is rewritten to the tool name reported by the module, so the affected rows also ended up with a different value in that column than the rows that kept their samplesheet statistics.
+
+    The branch now tests for absence, which is what the samplesheet schema expresses: `nf-schema` converts an empty field to `null`, so genuinely missing statistics still route to `GENOME_EVALUATION` while a provided `0` no longer does. This matches the `RNA_presence` test already used in the same workflow.
+
+  - The `genome_coverage` branch (`COVERM_GENOME`) is deliberately unchanged. Its schema field declares `exclusiveMinimum: 0`, so a samplesheet cannot supply `0` there, and an omitted value arrives as `null`, for which the truthiness test and a `null` test behave identically.
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.0 - 01/08/2026
 
 Initial release of nf-core/seqsubmit, created with the [nf-core](https://nf-co.re/) template.

diff --git a/README.md b/README.md
@@ -71,9 +71,9 @@ See the [`reads` mode section](docs/usage.md#samplesheet-input) of the usage doc
 Example:
 
 ```csv
-id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
-assembly_1,data/contigs_1.fasta.gz,data/reads_1.fastq.gz,data/reads_2.fastq.gz,,ERR011322,SPAdes,3.15.5
-assembly_2,data/contigs_2.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9
+id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version,assembly_type
+assembly_1,data/contigs_1.fasta.gz,data/reads_1.fastq.gz,data/reads_2.fastq.gz,,ERR011322,SPAdes,3.15.5,metagenome
+assembly_2,data/contigs_2.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9,metatranscriptome
 ```
 
 See the [`metagenomic_assemblies` mode section](docs/usage.md#samplesheet-input-1) of the usage documentation for more details.

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -58,6 +58,8 @@ custom_data:
         title: "Filepath"
       Sample:
         title: "Sample"
+      Library:
+        title: "Library"
 
   genome_metadata:
     id: "genome_metadata"

diff --git a/assets/schema_input_assembly.json b/assets/schema_input_assembly.json
@@ -92,6 +92,14 @@
                 "errorMessage": "Assembler version must be provided and cannot contain spaces",
                 "description": "Version of the assembler software used to generate the assembly, e.g. 1.0.0",
                 "meta": ["assembler_version"]
+            },
+            "assembly_type": {
+                "type": "string",
+                "enum": ["metagenome", "metatranscriptome"],
+                "errorMessage": "Assembly type should be metagenome or metatranscriptome",
+                "description": "Assembly type: metagenome or metatranscriptome. Written to the ENA manifest as ASSEMBLY_TYPE 'primary metagenome' or 'metatranscriptome'. Default: metagenome",
+                "default": "metagenome",
+                "meta": ["assembly_type"]
             }
         },
         "required": ["id", "fasta", "run_accession", "assembler", "assembler_version"],

diff --git a/conf/modules.config b/conf/modules.config
@@ -176,7 +176,15 @@ process {
         ]
     }
 
-    withName: 'REGISTERSTUDY|GENERATE_ASSEMBLY_MANIFEST|CREATE_READS_MANIFEST' {
+    withName: 'REGISTERSTUDY|CREATE_READS_MANIFEST' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: 'GENERATE_ASSEMBLY_MANIFEST' {
+        errorStrategy = { task.exitStatus in (1 + (130..145) + 104 + (175..177)) ? 'retry' : 'finish' }
+        maxRetries    = 3
         publishDir = [
             enabled: false
         ]

diff --git a/docs/usage.md b/docs/usage.md
@@ -214,21 +214,22 @@ You will need to create a samplesheet with information about the metagenomic ass
 Example:
 
 ```csv title="samplesheet_assembly.csv"
-id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
-assembly_001,data/assembly_001.fasta.gz,data/assembly_001_R1.fastq.gz,data/assembly_001_R2.fastq.gz,,ERR011322,SPAdes,3.15.5
-assembly_002,data/assembly_002.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9
+id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version,assembly_type
+assembly_001,data/assembly_001.fasta.gz,data/assembly_001_R1.fastq.gz,data/assembly_001_R2.fastq.gz,,ERR011322,SPAdes,3.15.5,metagenome
+assembly_002,data/assembly_002.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9,metatranscriptome
 ```
 
-| Column              | Required    | Description                                                                                                                                           |
-| ------------------- | ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`                | Yes         | A unique identifier for this data entry. Must be globally unique within the input dataset.                                                            |
-| `fasta`             | Yes         | Path to assembly contigs in FASTA format compressed with `gzip`.                                                                                      |
-| `fastq_1`           | Conditional | Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if `coverage` is not provided.                             |
-| `fastq_2`           | No          | Path to the second read file in FASTQ format for paired-end data used to generate the source metagenomic assembly. Leave empty for single-end reads.  |
-| `coverage`          | Conditional | Estimated sequencing depth of the assembly. If this value is missing, it is computed automatically during pipeline execution when reads are provided. |
-| `run_accession`     | Yes         | ENA run accession for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA.                                    |
-| `assembler`         | Yes         | Name of the assembler software used to generate the assembly, e.g. MEGAHIT, SPAdes, metaSPAdes, Flye, etc.                                            |
-| `assembler_version` | Yes         | Version of the assembler software used to generate the assembly, e.g. 1.0.0.                                                                          |
+| Column              | Required    | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| ------------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`                | Yes         | A unique identifier for this data entry. Must be globally unique within the input dataset.                                                                                                                                                                                                                                                                                                                                                                                        |
+| `fasta`             | Yes         | Path to assembly contigs in FASTA format compressed with `gzip`.                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| `fastq_1`           | Conditional | Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if `coverage` is not provided.                                                                                                                                                                                                                                                                                                                                                         |
+| `fastq_2`           | No          | Path to the second read file in FASTQ format for paired-end data used to generate the source metagenomic assembly. Leave empty for single-end reads.                                                                                                                                                                                                                                                                                                                              |
+| `coverage`          | Conditional | Estimated sequencing depth of the assembly. If this value is missing, it is computed automatically during pipeline execution when reads are provided.                                                                                                                                                                                                                                                                                                                             |
+| `run_accession`     | Yes         | ENA run accession for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA.                                                                                                                                                                                                                                                                                                                                                                |
+| `assembler`         | Yes         | Name of the assembler software used to generate the assembly, e.g. MEGAHIT, SPAdes, metaSPAdes, Flye, etc.                                                                                                                                                                                                                                                                                                                                                                        |
+| `assembler_version` | Yes         | Version of the assembler software used to generate the assembly, e.g. 1.0.0.                                                                                                                                                                                                                                                                                                                                                                                                      |
+| `assembly_type`     | No          | Sequencing library source: `metagenome` for metagenome assembly (would be used as _'primary metagenome'_ in manifest file following [ENA docs](https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome/primary.html)) or `metatranscriptome` for metatranscriptome assembly (woule be used _'metatranscriptome'_ in assembly manifest following [ENA docs](https://ena-docs.readthedocs.io/en/latest/submit/assembly/metatranscriptome.html)). Default: `metagenome` |
 
 Provide either read files (`fastq_1`, optionally `fastq_2`) or a `coverage` value for each row. If `coverage` is missing and reads are provided, the workflow calculates average coverage with CoverM. See the [Methods documentation](docs/methods.md) for more information on how coverage is calculated.
 

diff --git a/modules/local/create_assembly_metadata_csv/main.nf b/modules/local/create_assembly_metadata_csv/main.nf
@@ -18,14 +18,15 @@ process CREATE_ASSEMBLY_METADATA_CSV {
     task.ext.when == null || task.ext.when
 
     script:
-    def header = 'Runs,Coverage,Assembler,Version,Filepath,Sample'
+    def header = 'Runs,Coverage,Assembler,Version,Filepath,Sample,Library'
     def row = [
         meta.run_accession,
         meta.coverage,
         meta.assembler,
         meta.assembler_version,
         fasta.name,
-        ''    // Sample column left empty because co-assemblies are not supported
+        '',    // Sample column left empty because co-assemblies are not supported
+        meta.assembly_type ?: 'metagenome'  // it would be applied by schema, but still needed as safe case for tests
     ].join(',')
     """
     cat <<-END_CSV > ${meta.id}_assembly_metadata.csv

diff --git a/modules/local/create_assembly_metadata_csv/meta.yml b/modules/local/create_assembly_metadata_csv/meta.yml
@@ -21,6 +21,7 @@ input:
           - coverage: Assembly coverage value
           - assembler: Name of the assembler used
           - assembler_version: Version of the assembler
+          - assembly_type: 'metagenome' or 'metatranscriptome' (optional, default: 'metagenome')
     - fasta:
         type: file
         description: Assembly FASTA file
@@ -34,7 +35,10 @@ output:
             Groovy Map containing sample information (same as input)
       - "*.csv":
           type: file
-          description: CSV file containing assembly metadata to be used as input for the assembly_uploader
+          description: |
+            CSV file containing assembly metadata to be used as input for the assembly_uploader,
+            with columns Runs, Coverage, Assembler, Version, Filepath, Sample (empty) and
+            Library (assembly_type value, defines ASSEMBLY_TYPE in the ENA manifest)
           pattern: "*_assembly_metadata.csv"
 
 authors:

diff --git a/modules/local/create_assembly_metadata_csv/tests/main.nf.test b/modules/local/create_assembly_metadata_csv/tests/main.nf.test
@@ -19,7 +19,8 @@ nextflow_process {
                         run_accession: 'ERR123456',
                         coverage: 50.5,
                         assembler: 'metaspades',
-                        assembler_version: '3.15.5'
+                        assembler_version: '3.15.5',
+                        assembly_type: 'metagenome'
                     ],
                     file('https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz')
                 ]
@@ -49,7 +50,8 @@ nextflow_process {
                         run_accession: 'ERR999999',
                         coverage: 75.0,
                         assembler: 'megahit',
-                        assembler_version: '1.2.9'
+                        assembler_version: '1.2.9',
+                        assembly_type: 'metatranscriptome'
                     ],
                     file('https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz')
                 ]

diff --git a/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap b/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap
@@ -9,9 +9,10 @@
                             "run_accession": "ERR123456",
                             "coverage": 50.5,
                             "assembler": "metaspades",
-                            "assembler_version": "3.15.5"
+                            "assembler_version": "3.15.5",
+                            "assembly_type": "metagenome"
                         },
-                        "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529"
+                        "test_sample_assembly_metadata.csv:md5,5627f0b0bc83720dd269e2ea8ac16eff"
                     ]
                 ],
                 "1": [
@@ -28,14 +29,15 @@
                             "run_accession": "ERR123456",
                             "coverage": 50.5,
                             "assembler": "metaspades",
-                            "assembler_version": "3.15.5"
+                            "assembler_version": "3.15.5",
+                            "assembly_type": "metagenome"
                         },
-                        "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529"
+                        "test_sample_assembly_metadata.csv:md5,5627f0b0bc83720dd269e2ea8ac16eff"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-07-07T13:48:39.201846",
+        "timestamp": "2026-10-15T11:45:01.123968",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -51,7 +53,8 @@
                             "run_accession": "ERR999999",
                             "coverage": 75.0,
                             "assembler": "megahit",
-                            "assembler_version": "1.2.9"
+                            "assembler_version": "1.2.9",
+                            "assembly_type": "metatranscriptome"
                         },
                         "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -70,14 +73,15 @@
                             "run_accession": "ERR999999",
                             "coverage": 75.0,
                             "assembler": "megahit",
-                            "assembler_version": "1.2.9"
+                            "assembler_version": "1.2.9",
+                            "assembly_type": "metatranscriptome"
                         },
                         "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-07-07T13:48:46.340926",
+        "timestamp": "2026-10-15T11:45:06.881317",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"

diff --git a/modules/local/generate_assembly_manifest/environment.yml b/modules/local/generate_assembly_manifest/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::assembly_uploader=1.3.5"
+  - "bioconda::assembly_uploader=1.3.6"
diff --git a/modules/local/generate_assembly_manifest/main.nf b/modules/local/generate_assembly_manifest/main.nf
@@ -4,8 +4,8 @@ process GENERATE_ASSEMBLY_MANIFEST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/assembly_uploader:1.3.5--pyhdfd78af_1':
-        'quay.io/biocontainers/assembly_uploader:1.3.5--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/assembly_uploader:1.3.6--pyhdfd78af_0':
+        'quay.io/biocontainers/assembly_uploader:1.3.6--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(assembly_fasta), path(data_csv)

diff --git a/modules/local/generate_assembly_manifest/meta.yml b/modules/local/generate_assembly_manifest/meta.yml
@@ -25,7 +25,7 @@ input:
         description: |
           CSV file containing metadata -
           runs (comma-separated and in quotes, example: "SRR1234,SRR5678"),
-          coverage, assembler, version, filepath and optionally sample.
+          coverage, assembler, version, filepath, [optionally] sample, [optionally] assembly_type
     - assembly_study:
         type: value
         description: |