ochkalova · Oct 20, 2026 · Oct 16, 2026 · Oct 16, 2026 · Oct 16, 2026 · Oct 16, 2026
diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,4 @@ null/
 .nf-test*
 .idea/
 test_data
+.venv
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,9 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#116](https://github.com/nf-core/seqsubmit/pull/116)
+  - All tests except the `*_existing_study` ones now register a new submission study, so they can be run with any Webin account ([#95](https://github.com/nf-core/seqsubmit/issues/95)). The `test_mag_complete_metadata_existing_study` and `test_assembly_complete_metadata_existing_study` tests submit to the existing study `PRJEB98843` and require maintainer Webin credentials
+  - `test_upload = true` is set explicitly in all test configs
+  - Study submission alias now has a random suffix, so parallel registrations started in the same second no longer collide
+  - `REGISTERSTUDY` now runs only when at least one input passed validation ([#113](https://github.com/nf-core/seqsubmit/issues/113))
 - [#106](https://github.com/nf-core/seqsubmit/pull/106)
   - Added support for metatranscriptome submission for ASSEMBLYSUBMIT
-  - Set retry to assembly_uploader
+  - Set retry to GENERATE_ASSEMBLY_MANIFEST module
 - [#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)

diff --git a/bin/submit_study.py b/bin/submit_study.py
@@ -13,6 +13,7 @@
 import logging
 import os
 import sys
+import uuid
 import xml.etree.ElementTree as ET
 from io import BytesIO
 from pathlib import Path
@@ -327,7 +328,8 @@ def build_submission_xml(
     # SUBMISSION_SET
     submission_set = ET.SubElement(webin, "SUBMISSION_SET")
     submission = ET.SubElement(submission_set, "SUBMISSION")
-    sub_alias = f"study-submission-{datetime.datetime.now().strftime('%Y%m%d-%H%M%S')}"
+    # Random suffix keeps aliases unique when several submissions start in the same second
+    sub_alias = f"study-submission-{datetime.datetime.now().strftime('%Y%m%d-%H%M%S')}-{uuid.uuid4().hex[:4]}"
     submission.set("alias", sub_alias)
     actions = ET.SubElement(submission, "ACTIONS")
     main_action = ET.SubElement(actions, "ACTION")

diff --git a/conf/test.config b/conf/test.config
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = params.pipelines_testdata_base_path + 'seqsubmit/test_data/small_cat_db/tax-db.tar.gz'
     checkm2_db       = null
-
 }
diff --git a/conf/test_assembly_complete_metadata.config b/conf/test_assembly_complete_metadata.config
@@ -20,14 +20,16 @@ process {
 
 params {
     config_profile_name        = 'Test --mode metagenomic_assemblies complete_metadata profile'
-   config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.'
+    config_profile_description = 'Single-case assembly test with complete metadata values provided'
 
     // Input data
     input  = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/assembly_complete_metadata.csv'
     outdir = 'test_output'
 
     mode             = "metagenomic_assemblies"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
+    test_upload      = true
 }
diff --git a/...ssembly_no_study_complete_metadata.config → ...y_complete_metadata_existing_study.config b/...ssembly_no_study_complete_metadata.config → ...y_complete_metadata_existing_study.config
@@ -20,16 +20,15 @@ process {
 
 params {
     config_profile_name        = 'Test --mode metagenomic_assemblies complete_metadata profile'
-    config_profile_description = 'Single-case assembly test with complete metadata values provided'
+    config_profile_description = 'Tests single assembly submission with all metadata provided in the samplesheet so the pipeline skips coverage calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study, so requires maintainer Webin credentials with access to PRJEB98843.'
 
     // Input data
     input  = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/assembly_complete_metadata.csv'
+    outdir = 'test_output'
 
     mode             = "metagenomic_assemblies"
-    submission_study = null
-    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
+    submission_study = "PRJEB98843"
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
-
 }
diff --git a/conf/test_assembly_no_coverage_paired_reads.config b/conf/test_assembly_no_coverage_paired_reads.config
@@ -27,7 +27,9 @@ params {
     outdir = 'test_output'
 
     mode             = "metagenomic_assemblies"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
+    test_upload      = true
 }
diff --git a/conf/test_assembly_no_coverage_single_reads.config b/conf/test_assembly_no_coverage_single_reads.config
@@ -27,7 +27,9 @@ params {
     outdir = 'test_output'
 
     mode             = "metagenomic_assemblies"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
+    test_upload      = true
 }
diff --git a/conf/test_assembly_one_contig.config b/conf/test_assembly_one_contig.config
@@ -27,7 +27,9 @@ params {
     outdir = 'test_output'
 
     mode             = "metagenomic_assemblies"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
+    test_upload      = true
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -16,9 +16,11 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true

diff --git a/...est_mag_no_study_complete_metadata.config → conf/test_mag_complete_metadata.config b/...est_mag_no_study_complete_metadata.config → conf/test_mag_complete_metadata.config
@@ -24,6 +24,7 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
     submission_study = null
@@ -34,5 +35,4 @@ params {
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_complete_metadata.conf → ...mag_complete_metadata_existing_study.conf b/conf/test_mag_complete_metadata.conf → ...mag_complete_metadata_existing_study.conf
@@ -20,10 +20,11 @@ process {
 
 params {
     config_profile_name        = 'Test --mode mags complete_metadata profile'
-    config_profile_description = 'Tests single MAG submission with all metadata provided in the samplesheet, so the pipeline skips statistics and taxonomy calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study.'
+    config_profile_description = 'Tests single MAG submission with all metadata provided in the samplesheet, so the pipeline skips statistics and taxonomy calculation and only performs the upload to ENA. Submits to a pre-existing ENA study passed via --submission_study, so requires maintainer Webin credentials with access to PRJEB98843.'
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_complete_metadata.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
     submission_study = "PRJEB98843"
@@ -33,5 +34,4 @@ params {
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_no_coverage_paired_reads.conf b/conf/test_mag_no_coverage_paired_reads.conf
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_paired_reads.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_no_coverage_single_reads.conf b/conf/test_mag_no_coverage_single_reads.conf
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_single_reads.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_no_quality.conf b/conf/test_mag_no_quality.conf
@@ -24,9 +24,11 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_quality.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
@@ -36,5 +38,4 @@ params {
     // which is not ideal but necessary to test the pipeline's behaviour with missing quality values
     // Track upstream issue here: https://github.com/chklovski/CheckM2/issues/140
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_no_rna_presence.conf b/conf/test_mag_no_rna_presence.conf
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_rna_presence.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_no_taxonomy.conf b/conf/test_mag_no_taxonomy.conf
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_taxonomy.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = params.pipelines_testdata_base_path + 'seqsubmit/test_data/small_cat_db/tax-db.tar.gz'
     checkm2_db       = null
-
 }
diff --git a/conf/test_mag_one_contig.conf b/conf/test_mag_one_contig.conf
@@ -24,14 +24,15 @@ params {
 
     // Input data
     input            = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_one_contig.csv'
+    outdir           = 'test_output'
 
     mode             = "mags"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true
 
     cat_db           = null
     checkm2_db       = null
-
 }
diff --git a/conf/test_reads_paired.config b/conf/test_reads_paired.config
@@ -27,7 +27,8 @@ params {
     outdir = 'test_output'
 
     mode             = "reads"
-    submission_study = "PRJEB98843"
+    submission_study = null
+    study_metadata   = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
     centre_name      = "TEST_CENTER"
 
     test_upload      = true

diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
@@ -230,7 +230,7 @@ All submissions are performed via [Webin-CLI](https://github.com/enasequence/web
 
 ### Testing Requirements
 
-All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA webin credentials. Contributors may ask for testing credentials on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel.
+All new functionality must be covered by tests. Running nf-tests that perform ENA submission locally requires ENA Webin credentials. Tests that register a new study can be run with any free [Webin account](https://www.ebi.ac.uk/ena/submit/webin/login); this is every test except the `*_existing_study` ones. The `*_existing_study` tests submit to the existing study `PRJEB98843` and need maintainer credentials, which contributors may ask for on the nf-core Slack [#seqsubmit](https://nfcore.slack.com/channels/seqsubmit) channel.
 
 At minimum, include:
 

diff --git a/nextflow.config b/nextflow.config
@@ -239,22 +239,22 @@ profiles {
         apptainer.runOptions    = '--nv'
         singularity.runOptions  = '--nv'
     }
-    test                                     { includeConfig 'conf/test.config' }
-    test_full                                { includeConfig 'conf/test_full.config' }
-    test_mag_complete_metadata               { includeConfig 'conf/test_mag_complete_metadata.conf' }
-    test_mag_no_study_complete_metadata      { includeConfig 'conf/test_mag_no_study_complete_metadata.config' }
-    test_mag_no_coverage_single_reads        { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' }
-    test_mag_no_coverage_paired_reads        { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' }
-    test_mag_no_quality                      { includeConfig 'conf/test_mag_no_quality.conf' }
-    test_mag_one_contig                      { includeConfig 'conf/test_mag_one_contig.conf' }
-    test_mag_no_rna_presence                 { includeConfig 'conf/test_mag_no_rna_presence.conf' }
-    test_mag_no_taxonomy                     { includeConfig 'conf/test_mag_no_taxonomy.conf' }
-    test_assembly_complete_metadata          { includeConfig 'conf/test_assembly_complete_metadata.config' }
-    test_assembly_no_study_complete_metadata { includeConfig 'conf/test_assembly_no_study_complete_metadata.config' }
-    test_assembly_no_coverage_single_reads   { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' }
-    test_assembly_no_coverage_paired_reads   { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' }
-    test_assembly_one_contig                 { includeConfig 'conf/test_assembly_one_contig.config' }
-    test_reads_paired                        { includeConfig 'conf/test_reads_paired.config' }
+    test                                           { includeConfig 'conf/test.config' }
+    test_full                                      { includeConfig 'conf/test_full.config' }
+    test_mag_complete_metadata_existing_study      { includeConfig 'conf/test_mag_complete_metadata_existing_study.conf' }
+    test_mag_complete_metadata                     { includeConfig 'conf/test_mag_complete_metadata.config' }
+    test_mag_no_coverage_single_reads              { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' }
+    test_mag_no_coverage_paired_reads              { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' }
+    test_mag_no_quality                            { includeConfig 'conf/test_mag_no_quality.conf' }
+    test_mag_one_contig                            { includeConfig 'conf/test_mag_one_contig.conf' }
+    test_mag_no_rna_presence                       { includeConfig 'conf/test_mag_no_rna_presence.conf' }
+    test_mag_no_taxonomy                           { includeConfig 'conf/test_mag_no_taxonomy.conf' }
+    test_assembly_complete_metadata_existing_study { includeConfig 'conf/test_assembly_complete_metadata_existing_study.config' }
+    test_assembly_complete_metadata                { includeConfig 'conf/test_assembly_complete_metadata.config' }
+    test_assembly_no_coverage_single_reads         { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' }
+    test_assembly_no_coverage_paired_reads         { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' }
+    test_assembly_one_contig                       { includeConfig 'conf/test_assembly_one_contig.config' }
+    test_reads_paired                              { includeConfig 'conf/test_reads_paired.config' }
 }
 
 // Load nf-core custom profiles from different institutions

diff --git a/tests/assembly_complete_metadata.nf.test.snap b/tests/assembly_complete_metadata.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "-profile test_assembly_complete_metadata": {
         "content": [
-            7,
+            8,
             {
                 "CONCAT_ACCESSIONS": {
                     "coreutils": 9.4,
@@ -22,6 +22,9 @@
                 "GENERATE_ASSEMBLY_MANIFEST": {
                     "assembly_uploader": "1.3.6"
                 },
+                "REGISTERSTUDY": {
+                    "mgnify-pipelines-toolkit": "1.5.1"
+                },
                 "SUBMIT": {
                     "ena-webin-cli": "9.0.3",
                     "mgnify-pipelines-toolkit": "1.5.1",

diff --git a/...sembly_no_study_complete_metadata.nf.test → ..._complete_metadata_existing_study.nf.test b/...sembly_no_study_complete_metadata.nf.test → ..._complete_metadata_existing_study.nf.test
@@ -1,13 +1,13 @@
 nextflow_pipeline {
 
-    name "Test assembly submission workflow - complete_metadata"
+    name "Test assembly submission workflow - complete_metadata (submission to existing study)"
     script "../main.nf"
     tag "pipeline"
     tag "mode_assembly"
-    tag "test_assembly_no_study_complete_metadata"
-    profile "test_assembly_no_study_complete_metadata"
+    tag "test_assembly_complete_metadata_existing_study"
+    profile "test_assembly_complete_metadata_existing_study"
 
-    test("-profile test_assembly_no_study_complete_metadata") {
+    test("-profile test_assembly_complete_metadata_existing_study") {
 
         when {
             params {
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,3 +11,4 @@ null/ @@
     .nf-test*
     .idea/
     test_data
+    .venv