Merge branch 'cjk-ani-threshold' of https://github.com/theiagen/publi…

…c_health_bioinformatics into cjk-ani-threshold
theiagen · Oct 10, 2023 · 5fdd8f0 · 5fdd8f0
2 parents 3e23ba7 + aea0235
commit 5fdd8f0
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Showing 7 changed files with 14 additions and 2 deletions.
diff --git a/tasks/utilities/task_broad_terra_tools.wdl b/tasks/utilities/task_broad_terra_tools.wdl
@@ -99,6 +99,7 @@ task export_taxon_tables {
     String? kmerfinder_query_coverage
     String? kmerfinder_template_coverage
     String? kmerfinder_database
+    String? ani_docker
     File? amrfinderplus_all_report
     File? amrfinderplus_amr_report
     File? amrfinderplus_stress_report
@@ -603,6 +604,7 @@ task export_taxon_tables {
       "kmerfinder_query_coverage": "~{kmerfinder_query_coverage}",
       "kmerfinder_template_coverage": "~{kmerfinder_template_coverage}",
       "kmerfinder_database": "~{kmerfinder_database}",
+      "ani_docker": "~{ani_docker}",
       "resfinder_pheno_table": "~{resfinder_pheno_table}",
       "resfinder_pheno_table_species": "~{resfinder_pheno_table_species}",
       "resfinder_seqs": "~{resfinder_seqs}",

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -575,6 +575,7 @@
       contains: ["version", "fastq_scan", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/task_mummer_ani.wdl
       md5sum: 33a111c260b2fb0b6db6d9ed77ec8e87
+      md5sum: 33a111c260b2fb0b6db6d9ed77ec8e87
     - path: miniwdl_run/wdl/tasks/quality_control/task_ncbi_scrub.wdl
       contains: ["version", "scrub", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/task_qc_check_phb.wdl

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -545,6 +545,7 @@
       contains: ["version", "fastq_scan", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/task_mummer_ani.wdl
       md5sum: 33a111c260b2fb0b6db6d9ed77ec8e87
+      md5sum: 33a111c260b2fb0b6db6d9ed77ec8e87
     - path: miniwdl_run/wdl/tasks/quality_control/task_qc_check_phb.wdl
       contains: ["version", "qc_check_table", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/task_quast.wdl
@@ -600,9 +601,9 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
       md5sum: 024971d1439dff7d59c0a26a824bd2c6
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
-      md5sum: 43ef050bde1fb8755f38e697a1794918
+      md5sum: 1d7365ed0f29a7632568a37bfce0f1b6
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
-      md5sum: 24bfd35867f4ae864364e24195bf7f6f
+      md5sum: d144cb871c175029a34107a369e70c5d
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
       md5sum: 2614fac622fa2035b80a7b220b1aed86
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl

diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl
@@ -182,6 +182,7 @@ workflow theiaprok_fasta {
         kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage,
         kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage,
         kmerfinder_database = kmerfinder.kmerfinder_database,
+        ani_docker = ani.ani_docker,
         amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report,
         amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report,
         amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report,
@@ -436,6 +437,7 @@ workflow theiaprok_fasta {
     String? kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage
     String? kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage
     String? kmerfinder_database = kmerfinder.kmerfinder_database
+    String? ani_mummer_docker = ani.ani_docker
     # NCBI-AMRFinderPlus Outputs
     File amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report
     File amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
@@ -307,6 +307,7 @@ workflow theiaprok_illumina_pe {
             kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage,
             kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage,
             kmerfinder_database = kmerfinder.kmerfinder_database,
+            ani_docker = ani.ani_docker,
             amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report,
             amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report,
             amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report,
@@ -630,6 +631,7 @@ workflow theiaprok_illumina_pe {
     String? kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage
     String? kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage
     String? kmerfinder_database = kmerfinder.kmerfinder_database
+    String? ani_mummer_docker = ani.ani_docker
     # NCBI-AMRFinderPlus Outputs
     File? amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report
     File? amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -280,6 +280,7 @@ workflow theiaprok_illumina_se {
             kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage,
             kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage,
             kmerfinder_database = kmerfinder.kmerfinder_database,
+            ani_docker = ani.ani_docker,
             amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report,
             amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report,
             amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report,
@@ -582,6 +583,7 @@ workflow theiaprok_illumina_se {
     String? kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage
     String? kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage
     String? kmerfinder_database = kmerfinder.kmerfinder_database
+    String? ani_mummer_docker = ani.ani_docker
     # NCBI-AMRFinderPlus Outputs
     File? amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report
     File? amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report

diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl
@@ -278,6 +278,7 @@ workflow theiaprok_ont {
             kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage,
             kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage,
             kmerfinder_database = kmerfinder.kmerfinder_database,
+            ani_docker = ani.ani_docker,
             amrfinderplus_all_report = amrfinderplus.amrfinderplus_all_report,
             amrfinderplus_amr_report = amrfinderplus.amrfinderplus_amr_report,
             amrfinderplus_stress_report = amrfinderplus.amrfinderplus_stress_report,
@@ -556,6 +557,7 @@ workflow theiaprok_ont {
     String? kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage
     String? kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage
     String? kmerfinder_database = kmerfinder.kmerfinder_database
+    String? ani_mummer_docker = ani.ani_docker
     # NCBI-AMRFinderPlus Outputs
     File? amrfinderplus_all_report = amrfinderplus.amrfinderplus_all_report
     File? amrfinderplus_amr_report = amrfinderplus.amrfinderplus_amr_report