Fix download action

.github/workflows/download_pipeline.yml

@@ -18,6 +18,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  WEBIN_ACCOUNT: ${{ secrets.WEBIN_ACCOUNT }}
+  WEBIN_PASSWORD: ${{ secrets.WEBIN_PASSWORD }}
 
 jobs:
   configure:
@@ -32,7 +34,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || github.head_ref || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest
@@ -97,13 +99,20 @@ jobs:
           echo "Initial container image count: $image_count"
           echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
+      - name: Configure Nextflow secrets
+        shell: bash
+        run: |
+          nextflow secrets set ENA_WEBIN "$WEBIN_ACCOUNT"
+          nextflow secrets set ENA_WEBIN_PASSWORD "$WEBIN_PASSWORD"
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}

.github/workflows/nf-test.yml

@@ -83,8 +83,6 @@ jobs:
           - "25.10.4"
           - "latest-everything"
     env:
-      WEBIN_ACCOUNT: ${{ secrets.WEBIN_ACCOUNT }}
-      WEBIN_PASSWORD: ${{ secrets.WEBIN_PASSWORD }}
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
@@ -100,8 +98,6 @@ jobs:
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
           NXF_VERSION: ${{ matrix.NXF_VER }}
-          WEBIN_ACCOUNT: ${{ secrets.WEBIN_ACCOUNT }}
-          WEBIN_PASSWORD: ${{ secrets.WEBIN_PASSWORD }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}

.nf-core.yml

@@ -13,7 +13,7 @@ lint:
 nf_core_version: 4.0.2
 repository_type: pipeline
 template:
-  author: Martin Beracochea, Ekaterina Sakharova, Sofia Ochkalova, Evangelos Karatzas
+  author: Martin Beracochea, Ekaterina Sakharova, Sofia Ochkalova, Evangelos Karatzas, Tim Rozday
   description: Submit sequences, assemblies, MAGs, etc., to public archives
   force: false
   is_nfcore: true

modules/local/count_rna/main.nf

@@ -33,6 +33,6 @@ process COUNT_RNA {
 
     stub:
     """
-    echo -e "genome\tYes" > ${meta.id}_rna_decision.tsv
+    touch ${meta.id}_rna_decision.tsv
     """
 }

modules/local/count_rna/tests/main.nf.test.snap

@@ -23,14 +23,14 @@
                     {
                         "id": "test"
                     },
-                    "test_rna_decision.tsv:md5,cf8ebf06bf0641ceec14c8b034c639af"
+                    "test_rna_decision.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ]
         ],
-        "timestamp": "2026-06-25T21:38:27.45503",
+        "timestamp": "2026-07-01T18:37:30.337186",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.1"
         }
     }
 }

modules/local/genome_upload/main.nf

@@ -48,7 +48,7 @@ process GENOME_UPLOAD {
 
     stub:
     """
-    mkdir results/MAG_upload
+    mkdir -p results/MAG_upload
     touch results/MAG_upload/ENA_backup.json
     touch results/MAG_upload/genome_samples.xml
     touch results/MAG_upload/submission.xml

modules/local/registerstudy/main.nf

@@ -9,7 +9,7 @@ process REGISTERSTUDY {
 
     // ENA_WEBIN and ENA_WEBIN_PASSWORD must be set in the process environment.
     // In the pipeline, map Nextflow secrets via conf/modules.config or nextflow.config:
-    //   env { ENA_WEBIN = secrets.WEBIN_ACCOUNT; ENA_WEBIN_PASSWORD = secrets.WEBIN_PASSWORD }
+    //   env { ENA_WEBIN = secrets.ENA_WEBIN; ENA_WEBIN_PASSWORD = secrets.ENA_WEBIN_PASSWORD }
 
     input:
     tuple val(meta), path(study_metadata)

modules/local/registerstudy/tests/nextflow.config

@@ -3,8 +3,7 @@
 // --validate : validate and build XML but do not submit to ENA
 //
 // Dummy credentials are sufficient for --validate mode since
-// no HTTP calls are made. For real submission tests, replace with secrets:
-//   env { ENA_WEBIN = secrets.WEBIN_ACCOUNT; ENA_WEBIN_PASSWORD = secrets.WEBIN_PASSWORD }
+// no HTTP calls are made. For real submission tests, use Nextflow secrets
 
 env {
     ENA_WEBIN          = secrets.ENA_WEBIN

workflows/genomesubmit.nf

@@ -128,9 +128,11 @@ workflow GENOMESUBMIT {
     // Update metadata for records missing coverage
     fasta_updated_with_coverage = COVERM_GENOME.out.coverage.join(branched_coverage_results.genome_coverage_ref_input)
         .map{ meta, coverage_tsv, fasta ->
-              def coverage = coverage_tsv.readLines()[1].split('\t')[1];  // skip header
+              def lines = coverage_tsv.readLines()
+              // support for empty coverage files required for -stub mode
+              def coverage = lines ? lines[1].split('\t')[1] : null
               def updated_meta = meta.clone()
-              updated_meta.genome_coverage = coverage;
+              updated_meta.genome_coverage = coverage
               return [updated_meta, fasta]
         }
         .mix(branched_coverage_results.genome_coverage_present)
@@ -153,9 +155,11 @@ workflow GENOMESUBMIT {
     // Update metadata for records missing RNA
     fasta_updated_with_rna = RNA_DETECTION.out.rna_detected.join(branched_rna_results.rna_prediction_input)
         .map{ meta, rna_decision, fasta ->
-              def decision = rna_decision.readLines()[0].split('\t')[1];
+              def lines = rna_decision.readLines()
+              // support for empty decision files required for -stub mode
+              def decision = lines ? lines[0].split('\t')[1] : null
               def updated_meta = meta.clone()
-              updated_meta.RNA_presence = decision;
+              updated_meta.RNA_presence = decision
               return [updated_meta, fasta]
         }
         .mix(branched_rna_results.rna_present)
@@ -192,12 +196,12 @@ workflow GENOMESUBMIT {
         .join(branched_stats_results.genome_evaluation_input)
         .combine(stats_version_ch)
         .map { meta, stats_tsv, fasta, stats_version ->
-            def line = stats_tsv.readLines()[1].split('\t')
+            def lines = stats_tsv.readLines()
+            // support for empty checkm files required for -stub mode
             def updated_meta = meta.clone()
-            updated_meta.completeness = line[1]
-            updated_meta.contamination = line[2]
+            updated_meta.completeness = lines ? lines[1].split('\t')[1] : null
+            updated_meta.contamination = lines ? lines[1].split('\t')[2] : null
             updated_meta.stats_generation_software = stats_version
-
             return [updated_meta, fasta]
         }
         .mix(branched_stats_results.evaluation_present)
@@ -236,9 +240,10 @@ workflow GENOMESUBMIT {
     fasta_updated_with_taxonomy = FASTA_CLASSIFY_CATPACK.out.bat_classification
         .join(branched_taxonomy_results.genome_taxonomy_input)
         .map { meta, taxa_tsv, fasta ->
-            def line = taxa_tsv.readLines()[1].split('\t')
+            def lines = taxa_tsv.readLines()
             def updated_meta = meta.clone()
-            updated_meta.NCBI_lineage = line[3]
+            // support for empty taxonomy files required for -stub mode
+            updated_meta.NCBI_lineage = lines ? lines[1].split('\t')[3] : null
             return [updated_meta, fasta]
         }
         .mix(branched_taxonomy_results.taxonomy_present)