diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index 5c6ad15b3..58f0b6fb4 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -70,81 +70,6 @@
       md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
     - path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/101957at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102178at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102360at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98221at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98657at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99236at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99734at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99842at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1009041at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1024388at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1036075at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1043239at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/961486at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/981870at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/984717at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/fragmented_busco_sequences/108145at2157.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/fragmented_busco_sequences/108145at2157.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84219at2157.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/busco_sequences/single_copy_busco_sequences/84219at2157.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/101957at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102178at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102360at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99734at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99842at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1827334at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1211060at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1009041at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1024388at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1036075at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/961486at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/981870at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/984717at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/placement_files/marker_genes.fasta
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/logs/busco.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_out.log
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.faa
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.fna
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index 39a78ebe1..06caae04d 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -70,76 +70,6 @@
       md5sum: 3cfdda0096f0689c9829ed27bdef6b1a
     - path: miniwdl_run/call-busco/work/_miniwdl_inputs/0/test_contigs.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-busco/work/busco_downloads/file_versions.tsv
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/101957at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102178at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/102360at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98221at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/98657at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99236at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99734at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/hmms/99842at2157.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/archaea_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/ancestral_variants
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/dataset.cfg
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1009041at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1024388at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1036075at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/1043239at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/961486at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/981870at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/hmms/984717at2.hmm
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/ogs.id.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/info/species.info
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/lengths_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/links_to_ODB10.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/lineages/bacteria_odb10/scores_cutoff
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk
-    - path: miniwdl_run/call-busco/work/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/101957at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102178at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/102360at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99734at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/hmmer_output/99842at2157.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_archaea_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1540940at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1505038at2.faa
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/full_table.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1009041at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1024388at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/1036075at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/961486at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/981870at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/hmmer_output/984717at2.out
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/missing_busco_list.tsv
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/placement_files/marker_genes.fasta
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.json
-    - path: miniwdl_run/call-busco/work/test/auto_lineage/run_bacteria_odb10/short_summary.txt
-    - path: miniwdl_run/call-busco/work/test/logs/busco.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/hmmsearch_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/prodigal_out.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_err.log
-    - path: miniwdl_run/call-busco/work/test/logs/sepp_out.log
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.faa
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/predicted.fna
     - path: miniwdl_run/call-busco/work/test/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa