Merge pull request #422 from microbiomedata/398-genomad-output-directory-error

added proj_name for virusPlasmids workflow to metagenome pipeline template

Author: mflynn-lanl

data/workflow/templates/metagenome_pipeline_inputs.tmpl

@@ -11,6 +11,7 @@
    "main_workflow.metaAssembly_rename_contig_prefix":<PREFIX>,
    "main_workflow.metaAssembly_outdir":<METAASSEMBLY_OUTDIR>,
    "main_workflow.virusPlasmid_outdir":<VIRUSPLASMID_OUTDIR>,
+   "main_workflow.virusPlasmid_proj_name":<PREFIX>,
    "main_workflow.metaAnnotation_outdir":<METAANNOTATION_OUTDIR>,
    "main_workflow.metaAnnotation_imgap_project_id":<PREFIX>,
    "main_workflow.metaAnnotation_opaver_web_path":<OPAVER_WEB_DIR>,

data/workflow/templates/metagenome_pipeline_wdl.tmpl

@@ -59,6 +59,7 @@ workflow main_workflow {
         String virusPlasmid_outdir
         Int    virusPlasmid_cpu=8
         String virusPlasmid_database_location="/refdata"
+        String virusPlasmid_proj_name
         # MetaAnnotation
         String  metaAnnotation_imgap_project_id
         Int     metaAnnotation_additional_threads=8
@@ -201,6 +202,7 @@ workflow main_workflow {
     call viralPlasmid.viral as viralPlasmid_call {
         input:
             fasta=metaAssembly_contig,
+            proj_name=virusPlasmid_proj_name,
             outdir=virusPlasmid_outdir,
             option=virusPlasmid_options,
             cpu=virusPlasmid_cpu,