<commit_before><commit_msg>Debugging adding files to work dir<commit_after>cwlVersion: v1.0
class: CommandLineTool
baseCommand: awe_blat_prot.py

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "aa sims blat"

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: userattr.json
        entry: |
         {
           "stage_id": "650",
           "stage_name": "protein.sims",
           "m5nr_sims_version": $(inputs.nr_version)",
           "data_type": "similarity",
           "file_format": "blast m8",
           "sim_type": "protein"
         }
      # - $(inputs.myFile)
      - ${var f =inputs.nr_dir.location.concat('/').concat(inputs.nr_prefix).concat('.1'); return f; }
      - ${var f =inputs.nr_dir.location.concat('/').concat(inputs.nr_prefix).concat('.2'); return f; }
      
   
      
     
stdout: out.log
stderr: error.log

inputs:
  input:
    type: File
    inputBinding:
      prefix: -i
  output:
    type: string
    inputBinding:
      prefix: -o
  nr_prefix:
    type: string
    doc: prefix for nr, expects *.1 and *.2
    default: md5nr
  nr_dir:
    type: Directory
    doc: Directory containing the db with prefix nr_prefix
  sort_dir:
    type: string?
    inputBinding:
      prefix: -d  
  nr_version:
    type: string
  myFile:
    type: File

 
        
                 
  
                        
outputs:
  sims:
    type: File
    outputBinding:
      glob: $(inputs.output)
  userattr:
    type: File
    outputBinding:
      glob: userattr.json
  stdout:
    type: stdout
  error: 
    type: stderr    
 
        
{'fraction_non_alphanumeric': 0.1104368932038835, 'fraction_numerical': 0.007281553398058253, 'mean_word_length': 2.076492537313433, 'pattern_counts': {'":': 6, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6422289', 'n_tokens_mistral': 557, 'n_tokens_neox': 533, 'n_words': 124}