[TheiaProk] Add emmtyper task for Streptococcus pyogenes

tasks/species_typing/streptococcus/task_emmtyper.wdl

@@ -1,5 +1,8 @@
 version 1.0
 
+# task adapted with some modifications from Neranjan Perera's GAS_identification task_emmtyper.wdl
+# https://github.com/neranjan007/GAS_identification/blob/454ef3b0cc8a90950b48342cde87136962f9adb1/tasks/task_emmtyper.wdl
+
 task emmtyper {
   meta {
     description: "emm-typing of Streptococcus pyogenes assemblies"
@@ -37,23 +40,30 @@ task emmtyper {
   }
   command <<<
     echo $(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//' | tee VERSION
+
     emmtyper \
-      ~{'--workflow' + wf} \
-      ~{'--cluster-distance' + cluster_distance} \
-      ~{'--percent-identity' + percid} \
-      ~{'--culling-limit' + culling_limit} \
-      ~{'--mismatch' + mismatch} \
-      ~{'--align-diff' + align_diff} \
-      ~{'--gap' + gap} \
-      ~{'--min-perfect' + min_perfect} \
-      ~{'--min-good' + min_good} \
-      ~{'--max-size' + max_size} \
+      ~{'--workflow ' + wf} \
+      ~{'--cluster-distance ' + cluster_distance} \
+      ~{'--percent-identity ' + percid} \
+      ~{'--culling-limit ' + culling_limit} \
+      ~{'--mismatch ' + mismatch} \
+      ~{'--align-diff ' + align_diff} \
+      ~{'--gap ' + gap} \
+      ~{'--min-perfect ' + min_perfect} \
+      ~{'--min-good ' + min_good} \
+      ~{'--max-size ' + max_size} \
+      --output-format verbose \
       ~{assembly} \
-      > ~{samplename}.tsv
+      > ~{samplename}_emmtyper.tsv
+
+      # emm type is in column 4 for verbose output format
+      awk -F "\t" '{print $4}' ~{samplename}_emmtyper.tsv > EMM_TYPE
   >>>
   output {
-    File emmtyper_results = "~{samplename}.tsv"
+    String emmtyper_emm_type = read_string("EMM_TYPE")
+    File emmtyper_results_tsv = "~{samplename}_emmtyper.tsv"
     String emmtyper_version = read_string("VERSION")
+    String emmtyper_docker = docker
   }
   runtime {
     docker: "~{docker}"

tasks/utilities/data_export/task_broad_terra_tools.wdl

@@ -312,6 +312,10 @@ task export_taxon_tables {
     String? seroba_ariba_serotype
     String? seroba_ariba_identity
     File? seroba_details
+    String? emmtyper_emm_type
+    File? emmtyper_results_tsv
+    String? emmtyper_version
+    String? emmtyper_docker
     String? emmtypingtool_emm_type
     File? emmtypingtool_results_xml
     String? emmtypingtool_version
@@ -722,6 +726,10 @@ task export_taxon_tables {
       "seroba_ariba_serotype": "~{seroba_ariba_serotype}",
       "seroba_ariba_identity": "~{seroba_ariba_identity}",
       "seroba_details": "~{seroba_details}",
+      "emmtyper_emm_type": "~{emmtyper_emm_type}",
+      "emmtyper_results_tsv": "~{emmtyper_results_tsv}",
+      "emmtyper_version": "~{emmtyper_version}",
+      "emmtyper_docker": "~{emmtyper_docker}",
       "emmtypingtool_emm_type": "~{emmtypingtool_emm_type}",
       "emmtypingtool_reults_xml": "~{emmtypingtool_results_xml}",
       "emmtypingtool_version": "~{emmtypingtool_version}",

tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml

@@ -631,11 +631,11 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 52556169654cfa3e5de47c1987e83475
+      md5sum: 14565031f96d01ee6480bb0f9d19551d
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
-      md5sum: 0b4ef1f3f2711a0460050a1a09d44911
+      md5sum: 646e726beb68fc61f84a428bf2fb7244
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 6c125054324cd3597f8291baefb54694
+      md5sum: 43367523b9140ca0d2ac15869046343c
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       contains: ["version", "QC", "output"]
     - path: miniwdl_run/workflow.log

tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml

@@ -594,11 +594,11 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 52556169654cfa3e5de47c1987e83475
+      md5sum: 14565031f96d01ee6480bb0f9d19551d
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
-      md5sum: e2015675a4f53e0e4492e8c6a43dcb37
+      md5sum: 347c054f9850e885e6a130d1655765d7
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: 6c125054324cd3597f8291baefb54694
+      md5sum: 43367523b9140ca0d2ac15869046343c
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: 963090bb29184f61c7025e2bc487de4b
     - path: miniwdl_run/workflow.log

workflows/theiaprok/wf_theiaprok_fasta.wdl

@@ -410,6 +410,10 @@ workflow theiaprok_fasta {
         seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype,
         seroba_ariba_identity = merlin_magic.seroba_ariba_identity,
         seroba_details = merlin_magic.seroba_details,
+        emmtyper_emm_type = merlin_magic.emmtyper_emm_type,
+        emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv,
+        emmtyper_version = merlin_magic.emmtyper_version,
+        emmtyper_docker = merlin_magic.emmtyper_docker,
         pasty_serogroup = merlin_magic.pasty_serogroup,
         pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage,
         pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments,
@@ -678,6 +682,11 @@ workflow theiaprok_fasta {
     String? poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version
     String? poppunk_version = merlin_magic.poppunk_version
     String? poppunk_docker = merlin_magic.poppunk_docker
+    # Streptococcus pyogenes Typing
+    String? emmtyper_emm_type = merlin_magic.emmtyper_emm_type
+    File? emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv
+    String? emmtyper_version = merlin_magic.emmtyper_version
+    String? emmtyper_docker = merlin_magic.emmtyper_docker
     # Haemophilus influenzae Typing
     String? hicap_serotype = merlin_magic.hicap_serotype
     String? hicap_genes = merlin_magic.hicap_genes

workflows/theiaprok/wf_theiaprok_illumina_pe.wdl

@@ -541,6 +541,10 @@ workflow theiaprok_illumina_pe {
             seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype,
             seroba_ariba_identity = merlin_magic.seroba_ariba_identity,
             seroba_details = merlin_magic.seroba_details,
+            emmtyper_emm_type = merlin_magic.emmtyper_emm_type,
+            emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv,
+            emmtyper_version = merlin_magic.emmtyper_version,
+            emmtyper_docker = merlin_magic.emmtyper_docker,
             emmtypingtool_emm_type = merlin_magic.emmtypingtool_emm_type,
             emmtypingtool_results_xml = merlin_magic.emmtypingtool_results_xml,
             emmtypingtool_version = merlin_magic.emmtypingtool_version,
@@ -973,6 +977,10 @@ workflow theiaprok_illumina_pe {
     String? seroba_ariba_identity = merlin_magic.seroba_ariba_identity
     File? seroba_details = merlin_magic.seroba_details
     # Streptococcus pyogenes Typing
+    String? emmtyper_emm_type = merlin_magic.emmtyper_emm_type
+    File? emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv
+    String? emmtyper_version = merlin_magic.emmtyper_version
+    String? emmtyper_docker = merlin_magic.emmtyper_docker
     String? emmtypingtool_emm_type = merlin_magic.emmtypingtool_emm_type
     File? emmtypingtool_results_xml = merlin_magic.emmtypingtool_results_xml
     String? emmtypingtool_version = merlin_magic.emmtypingtool_version

workflows/theiaprok/wf_theiaprok_illumina_se.wdl

@@ -504,6 +504,10 @@ workflow theiaprok_illumina_se {
             agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts,
             agrvate_version = merlin_magic.agrvate_version,
             agrvate_docker = merlin_magic.agrvate_docker,
+            emmtyper_emm_type = merlin_magic.emmtyper_emm_type,
+            emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv,
+            emmtyper_version = merlin_magic.emmtyper_version,
+            emmtyper_docker = merlin_magic.emmtyper_docker,
             midas_docker = read_QC_trim.midas_docker,
             midas_report = read_QC_trim.midas_report,
             midas_primary_genus = read_QC_trim.midas_primary_genus,
@@ -899,6 +903,11 @@ workflow theiaprok_illumina_se {
     String? poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version
     String? poppunk_version = merlin_magic.poppunk_version
     String? poppunk_docker = merlin_magic.poppunk_docker
+    # Streptococcus pyogenes Typing
+    String? emmtyper_emm_type = merlin_magic.emmtyper_emm_type
+    File? emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv
+    String? emmtyper_version = merlin_magic.emmtyper_version
+    String? emmtyper_docker = merlin_magic.emmtyper_docker
     # Haemophilus influenzae Typing
     String? hicap_serotype = merlin_magic.hicap_serotype
     String? hicap_genes = merlin_magic.hicap_genes

workflows/theiaprok/wf_theiaprok_ont.wdl

@@ -510,6 +510,10 @@ workflow theiaprok_ont {
             agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts,
             agrvate_version = merlin_magic.agrvate_version,
             agrvate_docker = merlin_magic.agrvate_docker,
+            emmtyper_emm_type = merlin_magic.emmtyper_emm_type,
+            emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv,
+            emmtyper_version = merlin_magic.emmtyper_version,
+            emmtyper_docker = merlin_magic.emmtyper_docker,
             pasty_serogroup = merlin_magic.pasty_serogroup,
             pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage,
             pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments,
@@ -882,6 +886,11 @@ workflow theiaprok_ont {
     String? poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version
     String? poppunk_version = merlin_magic.poppunk_version
     String? poppunk_docker = merlin_magic.poppunk_docker
+    # Streptococcus pyogenes Typing
+    String? emmtyper_emm_type = merlin_magic.emmtyper_emm_type
+    File? emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv
+    String? emmtyper_version = merlin_magic.emmtyper_version
+    String? emmtyper_docker = merlin_magic.emmtyper_docker
     # Haemophilus influenzae Typing
     String? hicap_serotype = merlin_magic.hicap_serotype
     String? hicap_genes = merlin_magic.hicap_genes

workflows/utilities/wf_merlin_magic.wdl

@@ -25,6 +25,7 @@ import "../../tasks/species_typing/salmonella/task_sistr.wdl" as sistr_task
 import "../../tasks/species_typing/staphylococcus/task_agrvate.wdl" as agrvate_task
 import "../../tasks/species_typing/staphylococcus/task_spatyper.wdl" as spatyper_task
 import "../../tasks/species_typing/staphylococcus/task_staphopiasccmec.wdl" as staphopia_sccmec_task
+import "../../tasks/species_typing/streptococcus/task_emmtyper.wdl" as emmtyper_task
 import "../../tasks/species_typing/streptococcus/task_emmtypingtool.wdl" as emmtypingtool_task
 import "../../tasks/species_typing/streptococcus/task_pbptyper.wdl" as pbptyper
 import "../../tasks/species_typing/streptococcus/task_poppunk_streppneumo.wdl" as poppunk_spneumo
@@ -51,6 +52,17 @@ workflow merlin_magic {
     Int? pasty_min_coverage
     String? hicap_docker_image
     String? pasty_docker_image
+    String? emmtyper_wf
+    Int? emmtyper_cluster_distance
+    Int? emmtyper_percid
+    Int? emmtyper_culling_limit
+    Int? emmtyper_mismatch
+    Int? emmtyper_align_diff
+    Int? emmtyper_gap
+    Int? emmtyper_min_perfect
+    Int? emmtyper_min_good
+    Int? emmtyper_max_size
+    String? emmtyper_docker_image
     String? emmtypingtool_docker_image
     String? shigeifinder_docker_image
     String? shigatyper_docker_image
@@ -338,6 +350,22 @@ workflow merlin_magic {
     }
   }
   if (merlin_tag == "Streptococcus pyogenes") {
+    call emmtyper_task.emmtyper {
+      input:
+        assembly = assembly,
+        samplename = samplename,
+        docker = emmtyper_docker_image,
+        wf = emmtyper_wf,
+        cluster_distance = emmtyper_cluster_distance,
+        percid = emmtyper_percid,
+        culling_limit = emmtyper_culling_limit,
+        mismatch = emmtyper_mismatch,
+        align_diff = emmtyper_align_diff,
+        gap = emmtyper_gap,
+        min_perfect = emmtyper_min_perfect,
+        min_good = emmtyper_min_good,
+        max_size = emmtyper_max_size,
+    }
     if (paired_end && !ont_data) {
       call emmtypingtool_task.emmtypingtool {
         input:
@@ -668,6 +696,10 @@ workflow merlin_magic {
     String? seroba_ariba_identity = seroba_task.seroba_ariba_identity
     File? seroba_details = seroba_task.seroba_details
     # Streptococcus pyogenes Typing
+    String? emmtyper_emm_type = emmtyper.emmtyper_emm_type
+    File? emmtyper_results_tsv = emmtyper.emmtyper_results_tsv
+    String? emmtyper_version = emmtyper.emmtyper_version
+    String? emmtyper_docker = emmtyper.emmtyper_docker
     String? emmtypingtool_emm_type = emmtypingtool.emmtypingtool_emm_type
     File? emmtypingtool_results_xml = emmtypingtool.emmtypingtool_results_xml
     String? emmtypingtool_version = emmtypingtool.emmtypingtool_version