Merge pull request #297 from theiagen/im-theiaprok-kraken-fix

[TheiaProk suite] Patch fix: change type of kraken2_report to be string in taxon_table task
theiagen · Jan 12, 2024 · efe6e46 · efe6e46
2 parents 21f7a58 + 8c64df9
commit efe6e46
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/tasks/utilities/task_broad_terra_tools.wdl b/tasks/utilities/task_broad_terra_tools.wdl
@@ -300,7 +300,7 @@ task export_taxon_tables {
     Float? midas_secondary_genus_abundance
     String? kraken2_version
     String? kraken2_docker
-    File? kraken2_report
+    String? kraken2_report
     File? bakta_gbff
     File? bakta_gff3
     File? bakta_tsv

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -632,7 +632,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
       md5sum: faacd87946ee3fbdf70f3a15b79ce547
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
-      md5sum: cc1371406a7e691e704d6d7fff786f48
+      md5sum: e7a4488aebdabf9ea15a16538d6c835c
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: 4c681a395a318f224d770e423b4c1d75
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -122,7 +122,6 @@
     - 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/1567535at2.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/1505038at2.faa
@@ -598,7 +597,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
       md5sum: faacd87946ee3fbdf70f3a15b79ce547
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
-      md5sum: cc1371406a7e691e704d6d7fff786f48
+      md5sum: e7a4488aebdabf9ea15a16538d6c835c
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: e7c45852e17b11f6e9ae69cd91d52688
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl