Merge pull request #177 from CDCgov/params-and-metadata-fix-ick4

Params and metadata fix ick4
CDCgov · Mar 6, 2024 · e7960f7 · e7960f7
2 parents b246352 + 8e52d10
commit e7960f7
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Showing 7 changed files with 34,108 additions and 14 deletions.
diff --git a/.gitignore b/.gitignore
@@ -89,6 +89,7 @@ bin/__pycache__
 /bin/table2asn
 /bin/config_files/
 /bin/config_files
+!/bin/config_files/default_config.yaml
 
 .DS_Store
 app/.DS_Store

diff --git a/assets/sample_fastas/variola/VARV_RZ10_3587_2.fasta b/assets/sample_fastas/variola/VARV_RZ10_3587_2.fasta
diff --git a/assets/sample_fastqs/Cdiphtheriae/CP040557.fasta b/assets/sample_fastqs/Cdiphtheriae/CP040557.fasta
diff --git a/bin/submission_create.py b/bin/submission_create.py
@@ -464,7 +464,7 @@ def create_genbank_table2asn(submission_dir, submission_name, submission_files_d
 	submission_status = "processed-ok"
 	submission_id = "Table2asn"
 	# Create a temp file to store the downloaded table2asn
-	table2asn_dir = PROG_DIR + "/table2asn"
+	table2asn_dir = os.getcwd() + "/table2asn"
 	# Download the table2asn
 	print("Downloading Table2asn.", file=sys.stdout)
 	download_table2asn(table2asn_dir=table2asn_dir)

diff --git a/conf/test_params.config b/conf/test_params.config
@@ -22,7 +22,7 @@ params {
                         ref_fasta_path  = "${projectDir}/assets/ref/varv_ref_v6.fasta"
                         meta_path       = "${projectDir}/assets/sample_metadata/VARV_metadata_Sample_Run_1.xlsx"
                         ref_gff_path    = "${projectDir}/assets/ref/varv_ref_v7.gff3"
-        	        repeat_library  = "${projectDir}/assets/ref/varv_ref_v6.fasta"
+        	        repeat_library  = "${projectDir}/assets/lib/varv_repeats_lib.fasta"
                 }
                 else  {
                         // FOR MPOX
@@ -182,8 +182,8 @@ params {
         */
         // general
         submission                     = true
-        genbank                        = true
-        sra                            = true
+        genbank                        = false
+        sra                            = false
         gisaid                         = false
         biosample                      = true
         organism                       = "OTHER"  // for GISAID submission, choices are <FLU,COV,OTHER>

diff --git a/modules/local/initial_submission/main_full.nf b/modules/local/initial_submission/main_full.nf
@@ -38,6 +38,8 @@ process SUBMISSION_FULL {
         --fasta_file $fasta_path \
         --gff_file $annotations_path \
         --table2asn $test_flag $send_email_flag
+
+    rm table2asn
     """
 
     output:

diff --git a/nextflow.config b/nextflow.config
@@ -29,20 +29,20 @@ params {
     // organism specific repeat library settings
     // if you want to add your own custom library, if you choose to use one of ours state 'varv' to use the 'varv' custom lib or 'mpox' to use the mpox custom lib
     if ( params.variola ) {
-	    params.repeat_lib = "${projectDir}/assets/lib/varv_repeats_lib.fasta"
+	    repeat_library = "${projectDir}/assets/lib/varv_repeats_lib.fasta"
     }
     // assumes mpox as default for repeatmasker liftoff subworkflow
     else {
-	    params.repeat_lib = "${projectDir}/assets/lib/MPOX_repeats_lib.fasta"
+	    repeat_library = "${projectDir}/assets/lib/MPOX_repeats_lib.fasta"
     } 
 
     // bacterial annotation params 
     bakta                  = false
 
     // submission params 
     submission             = true
-    genbank                = true
-    sra                    = true
+    genbank                = false
+    sra                    = false
     gisaid                 = false
     biosample              = true
     organism               = "OTHER" // for GISAID submission, choices are <FLU,COV,OTHER>
@@ -55,12 +55,10 @@ params {
     // general params
     help                     = false
     publish_dir_mode         = 'copy'
-    output_dir               = ""
-    overwrite_output         = false
+    output_dir               = "results"
     // To Do check if we need these three dirs
-    final_liftoff_output_dir = "liftoff"
-    bakta_output_dir         = ""
-    vadr_output_dir          = ""
+    bakta_output_dir         = "bakta_outputs"
+    vadr_output_dir          = "vadr_outputs"
     final_liftoff_output_dir = "liftoff_outputs"
     val_output_dir           = "validation_outputs"
 
@@ -92,6 +90,7 @@ params {
     bakta_db_path           = ""
     bakta_min_contig_length = 5
     bakta_threads           = 2
+    bakta_gram              = "?"
     bakta_genus             = 'N/A'
     bakta_species           = 'N/A'
     bakta_strain            = 'N/A'
@@ -102,6 +101,7 @@ params {
 
     // optional bakta params
     bakta_compliant           = ""
+    bakta_complete            = ""
     bakta_keep_contig_headers = ""
     bakta_prodigal_tf         = ""
     bakta_replicons           = ""