updated denim recipe

updated dengue_typing

Author: cimendes

flowcraft/generator/components/typing.py

@@ -133,19 +133,8 @@ def __init__(self, **kwargs):
         self.directives = {"dengue_typing": {
             "cpus": 4,
             "memory": "'4GB'",
-            "container": "flowcraft/dengue_typing",
-            "version": "v1.0-1"
+            "container": "flowcraft/seq_typing",
+            "version": "2.0-1"
         }}
 
-        self.params = {
-            "BD_sequence_file": {
-                "default": "'/dengue_DB/blast_db/GenotypesDENV_14-05-18.problematic_sequences_corrected.fasta.corrected.fasta.iupac_removed.fasta'",
-                "description":
-                    "Path to the DB sequence file. If Blast DB was already"
-                    "produced only provide the file that doesn't end with '.n*'."
-                    "If no blast DB is found for the DB sequence file, one will"
-                    "be created. If more than one Blast DB file is passed, a type"
-                    "for each file will be determined."
-            }
-        }
 

flowcraft/generator/recipes/denim.py

@@ -17,9 +17,9 @@ def __init__(self):
         self.pipeline_str = "integrity_coverage " \
                             "fastqc_trimmomatic " \
                             "filter_poly " \
-                            "remove_host " \
                             "bowtie " \
                             "retrieve_mapped " \
+                            "remove_host " \
                             "viral_assembly " \
                             "assembly_mapping " \
                             "pilon " \

flowcraft/generator/templates/dengue_typing.nf

@@ -1,5 +1,3 @@
-file(params.BD_sequence_file{{ param_id }}) ? params.BD_sequence_file{{ param_id }} : exit(1, "'BD_sequence_file{{ param_id }}' parameter missing")
-
 process dengue_typing_{{ pid }} {
 
     // Send POST request to platform
@@ -26,7 +24,7 @@ process dengue_typing_{{ pid }} {
         cp -r /NGStools/ReMatCh rematch_temp
         export PATH="\$(pwd)/rematch_temp/ReMatCh:\$PATH"
 
-        seq_typing.py assembly -f ${assembly} -b ${ params.BD_sequence_file{{ param_id }} } -o ./ -j $task.cpus -t nucl
+        seq_typing.py assembly --org Dengue Virus -f ${assembly} -o ./ -j $task.cpus -t nucl
 
         # Add information to dotfiles
         json_str="{'tableRow':[{'sample':'${sample_id}','data':[{'header':'seqtyping','value':'\$(cat seq_typing.report.txt)','table':'typing'}]}],'metadata':[{'sample':'${sample_id}','treeData':'\$(cat seq_typing.report.txt)','column':'typing'}]}"