Fix tests

.github/workflows/download_pipeline.yml

@@ -89,6 +89,11 @@ jobs:
           echo "Initial container image count: $image_count"
           echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
+      - name: Download busco data
+        # Download A busco subset for the fungal test data set that is full enough to show some real output.
+        run: |
+          curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/busco.tar.gz | tar xzf -
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true

assets/TreeValTinyFullSangerTest.yaml

@@ -0,0 +1,37 @@
+assembly:
+  assem_level: scaffold
+  sample_id: grTriPseu1
+  latin_name: to_provide_taxonomic_rank
+  defined_class: fungi
+  assem_version: 1
+  project_id: DTOL
+reference_file: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa
+map_order: length
+assem_reads:
+  read_type: hifi
+  read_data:
+    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/pacbio/seqkitPacbio50000.fasta.gz
+  supplementary_data: path
+hic_data:
+  hic_cram:
+    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-1000.cram
+    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-2000.cram
+  hic_aligner: bwamem2
+kmer_profile:
+  # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir
+  kmer_length: 31
+  profile: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData
+alignment:
+  genesets:
+    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/gene_alignment_data/fungi/csv_data/LaetiporusSulphureus.gfLaeSulp1-data.csv
+self_comp:
+  motif_len: 0
+intron:
+  size: "50k"
+telomere:
+  teloseq: TTAGGG
+synteny:
+  - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/synteny/fungi/LaetiporusSulphureus.fasta
+busco:
+  lineages_path: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/busco/subset/
+  lineage: fungi_odb10

conf/test_full.config

@@ -27,6 +27,6 @@ params {
     config_profile_name        = "FULL local test profile"
     config_profile_description = "FULL test dataset to check pipeline function, using a current full local dataset"
 
-    input = "${projectDir}/assets/TreeValTinyFullTest.yaml"
+    input = "${projectDir}/assets/TreeValTinyFullSangerTest.yaml"
     mode = "FULL"
 }