AntiSmash to gff - refactor.

Removed the dependency of the json file.

Author: mberacochea

tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash-subwf.cwl

@@ -18,9 +18,6 @@ inputs:
     accession: string
 
 outputs:
-  antismash_js:
-    type: File
-    outputSource: fix_geneclusters_json/fixed_js
   antismash_txt:
     type: File
     outputSource: fix_geneclusters_txt/fixed_txt
@@ -43,7 +40,6 @@ steps:
         source: fasta_file
         valueFrom: $(self.nameext)
     out:
-      - geneclusters_js
       - geneclusters_txt
       - embl_file
       - gbk_file
@@ -71,22 +67,3 @@ steps:
         source: fasta_file
         valueFrom: $(self.basename).gncl.txt
     out: [ fixed_txt ]
-
-  # convert js to json
-  antismash_json_generation:
-    run: post-processing/json_generation/antismash_json_generation.cwl
-    in:
-      input_js: run_antismash/geneclusters_js
-      outputname: {default: 'geneclusters.json'}
-    out: [ output_json ]
-
-  # change json
-  fix_geneclusters_json:
-    run: post-processing/fix_geneclusters_js/change_geneclusters_js.cwl
-    in:
-      input_geneclusters_js: antismash_json_generation/output_json
-      output_filename:
-        source: fasta_file
-        valueFrom: $(self.basename).gncl.json
-      accession: accession
-    out: [ fixed_js ]

tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_chunking_subwf.cwl

@@ -73,18 +73,10 @@ steps:
         source: filtered_fasta
         valueFrom: $(self.nameroot)
     out:
-      - antismash_js
       - antismash_txt
       - antismash_gbk
       - antismash_embl
 
-  unite_geneclusters_json:
-    run: post-processing/json_generation/json_fix_subwf.cwl
-    in:
-      jsons: run_antismash/antismash_js
-      filtered_fasta: filtered_fasta
-    out: [ antismash_result_json ]
-
   unite_geneclusters_txt:
     run: ../../../../utils/concatenate.cwl
     in:
@@ -126,7 +118,6 @@ steps:
     in:
       antismash_geneclus: antismash_summary/reformatted_clusters
       antismash_embl: unite_embl/result
-      antismash_gc_json: unite_geneclusters_json/antismash_result_json
       output_name:
         source: filtered_fasta
         valueFrom: $(self.nameroot).antismash.gff

tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/GFF_antismash/antismash_to_gff.cwl

@@ -13,7 +13,7 @@ hints:
   DockerRequirement:
     dockerPull: alpine:3.9.4
 
-baseCommand: [antismash_to_gff.py]
+baseCommand: [antismash_to_gff_nojson.py]
 
 inputs:
   antismash_geneclus:
@@ -24,10 +24,6 @@ inputs:
     type: File
     inputBinding:
       prefix: -e
-  antismash_gc_json:
-    type: File
-    inputBinding:
-      prefix: -j
   output_name:
     type: string
     inputBinding:

tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/GFF_antismash/antismash_to_gff.py

@@ -4,7 +4,4 @@ antismash_geneclus:
 antismash_embl:
   class: File
   path: ../antismash/expected-output/assembly-SRR1620013_small_FASTA_FASTA_antismash_final.embl.gz
-antismash_gc_json:
-  class: File
-  path: ../../../input_examples/assembly/geneclusters.json
 output_name: assembly-SRR1620013_small_FASTA_FASTA.antismash.gff