Merge pull request #29 from microbiomedata/v1-mapping

v1.0 with mapping
microbiomedata · Jul 1, 2024 · ecef194 · ecef194
2 parents 1476a67 + e61f9ae
commit ecef194
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Showing 16 changed files with 1,258 additions and 62,091 deletions.
diff --git a/annotation.wdl b/annotation.wdl
@@ -1,22 +1,21 @@
+version 1.0
 import "structural-annotation.wdl" as sa
 import "functional-annotation.wdl" as fa
 
 workflow annotation {
-  String   cmzscore
-  File    imgap_input_fasta
-  String  imgap_project_id="GaXXXXXXX_contigs.fna"
-  String database_location="/refdata/img/"
-  String  imgap_project_type="metagenome"
-  Int     additional_threads=16
-
-  # structural annotation
-  Boolean sa_execute=true
-  # functional annotation
-  Boolean fa_execute=true
+  input {
+    String   cmzscore
+    File    imgap_input_fasta
+    String  imgap_project_id="GaXXXXXXX_contigs.fna"
+    String database_location="/refdata/img/"
+    String  imgap_project_type="metagenome"
+    Int     additional_threads=16
+    
+    Int?    fa_approx_num_proteins
+    String? gm_license
+    }
 
-  Int?    fa_approx_num_proteins
-  File? gm_license
-  if(sa_execute) {
+
       call sa.s_annotate {
         input:
           imgap_input_fasta = imgap_input_fasta,
@@ -27,9 +26,8 @@ workflow annotation {
           database_location = database_location,
           gm_license = gm_license
       }
-    }
+
 
-    if(fa_execute) {
       call fa.f_annotate {
         input:
           imgap_project_id = imgap_project_id,
@@ -40,6 +38,46 @@ workflow annotation {
           database_location = database_location,
           sa_gff = s_annotate.gff
       }
-
+  output{
+    File  sa_gff = s_annotate.gff
+    File? crt_gff = s_annotate.crt_gff
+    File? crisprs = s_annotate.crisprs 
+    File? crt_out = s_annotate.crt_out
+    File? genemark_gff = s_annotate.genemark_gff
+    File? genemark_genes = s_annotate.genemark_genes
+    File? genemark_proteins = s_annotate.genemark_proteins 
+    File? prodigal_gff = s_annotate.prodigal_gff
+    File? prodigal_genes = s_annotate.prodigal_genes
+    File? prodigal_proteins = s_annotate.prodigal_proteins
+    File? cds_gff = s_annotate.cds_gff
+    File? cds_proteins = s_annotate.cds_proteins
+    File? cds_genes = s_annotate.cds_genes
+    File? trna_gff = s_annotate.trna_gff
+    File? trna_bacterial_out = s_annotate.trna_bacterial_out
+    File? trna_archaeal_out = s_annotate.trna_archaeal_out
+    File? rfam_gff = s_annotate.rfam_gff
+    File? rfam_tbl = s_annotate.rfam_tbl
+    File? proteins = s_annotate.proteins
+    File? genes = s_annotate.genes
+    File product_name_gff = f_annotate.gff
+    File product_name_tsv = f_annotate.product_name_tsv
+    File ko_tsv = f_annotate.ko_tsv
+    File ec_tsv = f_annotate.ec_tsv
+    File phylo_tsv = f_annotate.phylo_tsv
+    File ko_ec_gff = f_annotate.ko_ec_gff
+    File last_blasttab = f_annotate.last_blasttab
+    File lineage_tsv = f_annotate.lineage_tsv
+    File cog_gff = f_annotate.cog_gff
+    File pfam_gff = f_annotate.pfam_gff
+    File tigrfam_gff = f_annotate.tigrfam_gff
+    File supfam_gff = f_annotate.supfam_gff
+    File smart_gff = f_annotate.smart_gff
+    File cath_funfam_gff = f_annotate.cath_funfam_gff
+    File cog_domtblout = f_annotate.cog_domtblout
+    File pfam_domtblout = f_annotate.pfam_domtblout
+    File tigrfam_domtblout = f_annotate.tigrfam_domtblout
+    File supfam_domtblout = f_annotate.supfam_domtblout
+    File smart_domtblout = f_annotate.smart_domtblout
+    File cath_funfam_domtblout = f_annotate.cath_funfam_domtblout
   }
 }