Validation + Submission Entrypoint (Issue #129)

conf/test_bacteria_params.config

@@ -35,6 +35,7 @@ params {
         run_submission = true
         run_bakta = true
         cleanup = true
+        run_annotation = true
 
         /*
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

conf/test_virus_params.config

@@ -43,7 +43,7 @@ params {
                 ANNOTATION SUBWORKFLOW 
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         */
-        run_submission = true
+        run_annotation = true
         run_vadr = false
 
         if ( params.variola ) {
@@ -134,6 +134,7 @@ params {
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         */
         // general
+        run_submission = true
         submission_output_dir = "submission_outputs"
         submission_prod_or_test = 'test'
         submission_wait_time = 'calc'

main.nf

@@ -63,6 +63,7 @@ include { RUN_SUBMISSION } from "$projectDir/subworkflows/entrypoints/submission
 include { RUN_INITIAL_SUBMISSION } from "$projectDir/subworkflows/entrypoints/initial_submission_entry"
 include { RUN_UPDATE_SUBMISSION } from "$projectDir/subworkflows/entrypoints/update_submission_entry"
 include { RUN_BAKTA } from "$projectDir/subworkflows/entrypoints/bakta_entry.nf"
+include { RUN_VALIDATION_AND_SUBMISSION } from "$projectDir/subworkflows/entrypoints/no_annotation"
 
 workflow only_validate_params {
     main:
@@ -148,4 +149,22 @@ workflow only_update_submission {
     main:
         // run subworkflow for update submission entrypoint
         RUN_UPDATE_SUBMISSION ()
+}
+
+workflow only_validation_and_submission {
+    main:
+        // calls subworkflow to run only validation and submission
+        RUN_VALIDATION_AND_SUBMISSION (
+            'dummy utility signal',
+            false
+        )
+}
+
+workflow only_validation_and_initial_submission {
+    main:
+        // calls subworkflow to run only validation and submission
+        RUN_VALIDATION_AND_SUBMISSION (
+            'dummy utility signal',
+            true
+        )
 }

subworkflows/entrypoints/no_annotation.nf

@@ -0,0 +1,70 @@
+#!/usr/bin/env nextflow 
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+                    SUBWORKFLOW FOR VALIDATION --> SUBMISSION
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { INITIALIZE_FILES                                  } from "../../modules/general_util/initialize_files/main"
+include { GET_WAIT_TIME                                     } from "../../modules/general_util/get_wait_time/main"
+include { METADATA_VALIDATION                               } from "../../modules/metadata_validation/main"
+include { SUBMISSION                                        } from "../../modules/submission/main"
+include { GENERAL_SUBMISSION                                } from "../submission"
+
+
+workflow RUN_VALIDATION_AND_SUBMISSION {
+
+    // Get the channel for the annotation files
+    if (!params.final_annotated_files_path.isEmpty()) {
+        annotationCh = Channel.fromPath("$params.final_annotated_files_path/*.gff")
+    }
+
+    take:
+        utility_signal
+        is_it_only_initial
+
+    main:
+
+        // initialize files (stage and change names for files)
+        INITIALIZE_FILES (
+            utility_signal
+        )
+
+        // run metadata validation process
+        METADATA_VALIDATION ( 
+            utility_signal,
+            params.meta_path
+        )
+
+        if ( is_it_only_initial == false ) {
+
+            // pre submission process + get wait time (parallel)
+            GET_WAIT_TIME (
+                METADATA_VALIDATION.out.tsv_Files.collect() 
+            )
+
+            // call the general submission workflow 
+            GENERAL_SUBMISSION (
+                METADATA_VALIDATION.out.tsv_Files.sort().flatten(),
+                INITIALIZE_FILES.out.fasta_files.sort().flatten(),
+                annotationCh,
+                params.submission_config, 
+                params.req_col_config, 
+                GET_WAIT_TIME.out 
+            )
+
+        } else {
+
+            // call submission process directly 
+            SUBMISSION (
+                METADATA_VALIDATION.out.tsv_Files.sort().flatten(),
+                INITIALIZE_FILES.out.fasta_files.sort().flatten(),
+                annotationCh, 
+                params.submission_config,
+                params.req_col_config,
+                'entry'
+            )
+
+        }
+}

workflows/main.nf

@@ -35,6 +35,7 @@ include { VADR_SUBMISSION                                   } from "../subworkfl
 include { BAKTA_SUBMISSION                                  } from "../subworkflows/submission"
 include { GENERAL_SUBMISSION                                } from "../subworkflows/submission"
 
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                     MAIN WORKFLOW
@@ -70,59 +71,63 @@ workflow MAIN_WORKFLOW {
         params.meta_path
     )
 
-    // run liftoff annotation process 
-    if ( params.run_liftoff == true ) {
-        LIFTOFF (
-            params.meta_path, 
-            INITIALIZE_FILES.out.fasta_dir, 
-            params.ref_fasta_path, 
-            params.ref_gff_path 
-        )
-    }
-
-    // run liftoff annotation process + repeatmasker 
-    if ( params.run_repeatmasker_liftoff == true ) {
+    // check if the user wants to skip annotation or not
+    if ( params.run_annotation == true ) {
 
-        // run repeatmasker annotation on files
-        RUN_REPEATMASKER_LIFTOFF (
-            RUN_UTILITY.out, 
-            fastaCh
-        )
-    }
+        // run liftoff annotation process 
+        if ( params.run_liftoff == true ) {
+            LIFTOFF (
+                params.meta_path, 
+                INITIALIZE_FILES.out.fasta_dir, 
+                params.ref_fasta_path, 
+                params.ref_gff_path 
+            )
+        }
 
-    // run vadr processes
-    if ( params.run_vadr == true ) {
-        RUN_VADR (
-            RUN_UTILITY.out, 
-            INITIALIZE_FILES.out.fasta_files.sort().flatten()
-        )
-    }
+        // run liftoff annotation process + repeatmasker 
+        if ( params.run_repeatmasker_liftoff == true ) {
 
-    // run bakta annotation process
-    if ( params.run_bakta == true ) {
-
-        if ( params.download_bakta_db ) {
-            BAKTADBDOWNLOAD ( RUN_UTILITY.out )
-            BAKTA (
-                RUN_UTILITY.out,
-                BAKTADBDOWNLOAD.out.db,
+            // run repeatmasker annotation on files
+            RUN_REPEATMASKER_LIFTOFF (
+                RUN_UTILITY.out, 
                 fastaCh
             )
+        }
 
-        } else {
+        // run vadr processes
+        if ( params.run_vadr == true ) {
+            RUN_VADR (
+                RUN_UTILITY.out, 
+                INITIALIZE_FILES.out.fasta_files.sort().flatten()
+            )
+        }
+
+        // run bakta annotation process
+        if ( params.run_bakta == true ) {
+
+            if ( params.download_bakta_db ) {
+                BAKTADBDOWNLOAD ( RUN_UTILITY.out )
+                BAKTA (
+                    RUN_UTILITY.out,
+                    BAKTADBDOWNLOAD.out.db,
+                    fastaCh
+                )
+
+            } else {
 
-            BAKTA (
-                RUN_UTILITY.out,
-                params.bakta_db_path,
+                BAKTA (
+                    RUN_UTILITY.out,
+                    params.bakta_db_path,
+                    fastaCh
+                )
+            }
+
+            BAKTA_POST_CLEANUP (
+                BAKTA.out.bakta_results,
+                params.meta_path,
                 fastaCh
-            )
+            )   
         }
-
-        BAKTA_POST_CLEANUP (
-            BAKTA.out.bakta_results,
-            params.meta_path,
-            fastaCh
-        )   
     }
 
     // run submission for the annotated samples 
@@ -133,8 +138,8 @@ workflow MAIN_WORKFLOW {
             METADATA_VALIDATION.out.tsv_Files.collect() 
         )
 
-         // check if all annotations are set to false 
-        if ([params.run_bakta, params.run_liftoff, params.run_vadr, params.run_repeatmasker_liftoff].any { it }) {
+        // check if all annotations are set to false 
+        if ( params.run_annotation == true ) {
 
             // call the submission workflow for liftoff 
             if ( params.run_liftoff == true ) {
@@ -183,7 +188,7 @@ workflow MAIN_WORKFLOW {
                     GET_WAIT_TIME.out   
                 )
             }  
-
+ 
         } else {
 
             // all annotations are false, therefore first check if user annotations are provided