Testing

sanger-tol · Sep 29, 2023 · c2c914b · c2c914b
1 parent 2fe5c54
commit c2c914b
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Showing 11 changed files with 6 additions and 346 deletions.
diff --git a/.github/assets/adaptivecard.json b/.github/assets/adaptivecard.json
diff --git a/.github/assets/email_template.html b/.github/assets/email_template.html
diff --git a/.github/assets/email_template.txt b/.github/assets/email_template.txt
diff --git a/.github/assets/methods_description_template.yml b/.github/assets/methods_description_template.yml
diff --git a/.github/assets/samplesheet.csv b/.github/assets/samplesheet.csv
diff --git a/.github/assets/schema_input.json b/.github/assets/schema_input.json
diff --git a/.github/assets/sendmail_template.txt b/.github/assets/sendmail_template.txt
diff --git a/.github/assets/slackreport.json b/.github/assets/slackreport.json
diff --git a/.github/assets/test-truth.yaml b/.github/assets/test-truth.yaml
diff --git a/.github/assets/test.yaml b/.github/assets/test.yaml
diff --git a/workflows/ascc.nf b/workflows/ascc.nf
@@ -77,10 +77,10 @@ workflow ASCC {
     //
     // SUBWORKFLOW: EXTRACT RESULTS HITS FROM TIARA
     //
-    EXTRACT_TIARA_HITS (
+/*     EXTRACT_TIARA_HITS (
         GENERATE_GENOME.out.reference_tuple
     )
-    ch_versions = ch_versions.mix(EXTRACT_TIARA_HITS.out.versions)
+    ch_versions = ch_versions.mix(EXTRACT_TIARA_HITS.out.versions) */
 
     //
     // LOGIC: INJECT SLIDING WINDOW VALUES INTO REFERENCE
@@ -100,23 +100,23 @@ workflow ASCC {
     //
     // SUBWORKFLOW: EXTRACT RESULTS HITS FROM NT-BLAST
     //
-    EXTRACT_NT_BLAST (
+/*     EXTRACT_NT_BLAST (
         modified_input,
         YAML_INPUT.out.nt_database,
         YAML_INPUT.out.ncbi_taxonomy_path,
         YAML_INPUT.out.ncbi_rankedlineage_path
     )
-    ch_versions = ch_versions.mix(EXTRACT_NT_BLAST.out.versions)
+    ch_versions = ch_versions.mix(EXTRACT_NT_BLAST.out.versions) */
 
     //
     // SUBWORKFLOW:
     //
-    RUN_NT_KRAKEN (
+/*     RUN_NT_KRAKEN (
         GENERATE_GENOME.out.reference_tuple,
         YAML_INPUT.out.nt_kraken_db_path,
         YAML_INPUT.out.ncbi_rankedlineage_path
     )
-    ch_versions = ch_versions.mix(RUN_NT_KRAKEN.out.versions)
+    ch_versions = ch_versions.mix(RUN_NT_KRAKEN.out.versions) */
 
     //
     // SUBWORKFLOW: COLLECT SOFTWARE VERSIONS