removed utility signal and cleanup files

conf/test_params.config

@@ -191,7 +191,7 @@ params {
         submission_prod_or_test        = "test" // "prod" if submitting
         submission_wait_time           = 'calc'
         send_submission_email          = false
-        submission_config              = "${projectDir}/bin/config_files/default_config.yaml" 
+        submission_config              = "${projectDir}/bin/config_files/config_kk.yaml" 
         submission_database            = "submit"  // must be either: 'submit' (follows existing config), 'genbank', 'sra', 'gisaid', 'biosample', 'joint_sra_biosample', or 'all'
         // batch_name                     = "batch1"
 

modules/local/liftoff_annotation/main.nf

@@ -14,7 +14,6 @@ process LIFTOFF {
     publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
 
     input:
-    val signal
     path meta_path
     path fasta_path
     path ref_fasta_path 

modules/local/liftoff_cli_annotation/main.nf

@@ -20,7 +20,6 @@ process LIFTOFF_CLI {
         }
 
 	input:
-    val signal
 	tuple val(meta), path(fasta)
     path ref_fasta_path 
     path ref_gff_path 

modules/local/metadata_validation/main.nf

@@ -17,7 +17,6 @@ process METADATA_VALIDATION {
     publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
 
     input:
-    val signal
     path meta_path
 
     script:

modules/local/post_bakta_annotation/main.nf

@@ -5,22 +5,11 @@
 */
 process BAKTA_POST_CLEANUP {
 
-<<<<<<< HEAD
-    //label 'main'
-
-    conda (params.enable_conda ? params.env_yml : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'staphb/tostadas:latest' :
-        'staphb/tostadas:latest' }"
-
-    publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
-=======
     conda (params.enable_conda ? params.env_yml : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'staphb/tostadas:latest' : 'staphb/tostadas:latest' }"
 
     // publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
->>>>>>> 883756c... cleaned up containers and publish dirs
 
     input:
     path bakta_results

modules/local/repeatmasker_annotation/main.nf

@@ -12,7 +12,6 @@ process REPEATMASKER {
         'quay.io/biocontainers/repeatmasker:4.1.5--pl5321hdfd78af_0'}"
 
 	input:
-	val signal
 	tuple val(meta), path(fasta_path)
 	path repeat_library
 

modules/local/update_submission/main.nf

@@ -13,8 +13,8 @@ process UPDATE_SUBMISSION {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'cdcgov/seqsender-dev' : 'cdcgov/seqsender-dev' }"
 
-    input:   
-    val wait_signal
+    input:
+    val wait
     path submission_config
     path submission_output
     path submission_log

modules/local/vadr_annotation/main.nf

@@ -12,7 +12,6 @@ process VADR {
         'staphb/vadr:latest' : 'staphb/vadr:latest' }"
 
     input:
-    val signal
 	tuple val(meta), path(fasta_path)
     path vadr_models_dir
 

subworkflows/local/bakta.nf

@@ -12,23 +12,19 @@ include { BAKTADBDOWNLOAD                                   } from "../../module
 
 workflow RUN_BAKTA {
     take: 
-    utility_signal
     fasta_ch
 
     main:
         if ( params.download_bakta_db ) {
             BAKTADBDOWNLOAD (
-                utility_signal 
                 )
             BAKTA (
-                utility_signal,
                 BAKTADBDOWNLOAD.out.db,
                 fasta_ch
                 )
             }
         else {
             BAKTA (
-            utility_signal,
             params.bakta_db_path,
             fasta_ch
             )

subworkflows/local/repeatmasker_liftoff.nf

@@ -13,19 +13,16 @@ include { CONCAT_GFFS                                       } from "../../module
 workflow REPEATMASKER_LIFTOFF {
 
     take:
-        utility_signal
         fasta
 
     main:
         // run repeatmasker annotation on files
         REPEATMASKER (
-           utility_signal,
            fasta,
            params.repeat_library
         )
         // run liftoff annotation on files
         LIFTOFF_CLI ( 
-            utility_signal,
             fasta,
             params.ref_fasta_path, 
             params.ref_gff_path 

subworkflows/local/vadr.nf

@@ -12,13 +12,11 @@ include { VADR_POST_CLEANUP                                 } from "../../module
 
 workflow RUN_VADR {
     take:
-        utility_signal
         fasta_files
 
     main:
         // run vadr processes
         VADR (
-            utility_signal, 
             fasta_files,
             params.vadr_models_dir
         )

workflows/tostadas.nf

@@ -8,7 +8,9 @@ nextflow.enable.dsl=2
 */
 // get the utility processes / subworkflows
 // include { CHECK_FILES                                       } from "../modules/local/general_util/check_files/main"
-include { RUN_UTILITY                                       } from "../subworkflows/local/utility"
+// include { RUN_UTILITY                                       } from "../subworkflows/local/utility"
+include { VALIDATE_PARAMS                                   } from '../modules/local/general_util/validate_params/main'
+
 include { GET_WAIT_TIME                                     } from "../modules/local/general_util/get_wait_time/main"
 
 // get metadata validation processes
@@ -41,29 +43,17 @@ include { WAIT                                          } from '../modules/local
 // To Do, create logic to run workflows for virus vs. bacteria
 workflow TOSTADAS {
 
-    // fastq_ch = 
-    // Channel.fromPath("$params.fastq_path").first()
-
-    // fasta_ch = 
-    // Channel.fromPath("${params.fasta_path}/*.fasta")
-    // .map { 
-    //      def meta = [:] 
-    //      meta['id'] = it.getSimpleName().replaceAll('_reformatted', '')
-    //      [ meta, it ] 
-    // }
-
     // check if help parameter is set
     if ( params.help == true ) {
         PRINT_PARAMS_HELP()
         exit 0
     }
 
-    // run utility subworkflow
-    RUN_UTILITY()
-
+    // validate params
+    VALIDATE_PARAMS()
+    
     // run metadata validation process
     METADATA_VALIDATION ( 
-        RUN_UTILITY.out,
         params.meta_path
     )
     // todo: the names of these tsv_Files need to be from sample name not fasta file name 
@@ -104,7 +94,6 @@ workflow TOSTADAS {
             if ( params.repeatmasker_liftoff ) {
              // run repeatmasker annotation on files
                 REPEATMASKER_LIFTOFF (
-                    RUN_UTILITY.out, 
                     fasta_ch
                 )
                 repeatmasker_gff_ch = REPEATMASKER_LIFTOFF.out.gff.collect().flatten()
@@ -122,7 +111,6 @@ workflow TOSTADAS {
             // run vadr processes
             if ( params.vadr ) {
                 RUN_VADR (
-                    RUN_UTILITY.out, 
                     fasta_ch
                 )
                 vadr_gff_ch = RUN_VADR.out.gff.collect().flatten()
@@ -138,7 +126,6 @@ workflow TOSTADAS {
         // run bakta annotation process
             if ( params.bakta == true ) {
                 RUN_BAKTA(
-                    RUN_UTILITY.out, 
                     fasta_ch
                 )
                 // set up submission channels
@@ -198,7 +185,6 @@ workflow TOSTADAS {
         // todo test update submission
         if ( params.update_submission ) {
             UPDATE_SUBMISSION (
-                RUN_UTILITY.out,
                 params.submission_config, 
                 INITIAL_SUBMISSION.out.submission_files
             )