diff --git a/wdl2cwl/tests/cwl_files/blast.cwl b/wdl2cwl/tests/cwl_files/blast.cwl
index 88f82107..fb588a4f 100644
--- a/wdl2cwl/tests/cwl_files/blast.cwl
+++ b/wdl2cwl/tests/cwl_files/blast.cwl
@@ -1,217 +1,335 @@
 cwlVersion: v1.2
-id: blast
-class: Workflow
-requirements:
-  - class: InlineJavascriptRequirement
-inputs:
-  - id: blast_docker_override
-    type:
-      - string
-      - 'null'
-  - id: blast_docker
-    type:
-      - string
-      - 'null'
-  - id: queryfa
-    type: File
-  - id: fname
-    default: /sfs/blastdb/2019_ncov/nucl/v6/ncov
-    type: string
-  - id: method
-    default: blastn
-    type: string
-  - id: outfmt
-    default: 7
-    type: int
-  - id: evalue
-    default: 10.0
-    type: float
-  - id: Outfile
-    type:
-      - string
-      - 'null'
-  - id: threads
-    default: 8
-    type: int
-  - id: runblastp.max_target_seqs
-    default: 100
-    type: int
-  - id: runblastp.word_size
-    default: 6
-    type: int
-  - id: runblastp.seg
-    default: no
-    type: string
-  - id: runblastp.comp_based_stats
-    default: '2'
-    type: string
-  - id: runblastp.matrix
-    default: BLOSUM62
-    type: string
-  - id: runblastp.gapopen
-    default: 11
-    type: int
-  - id: runblastp.gapextend
-    default: 1
-    type: int
-  - id: runblastp.max_hsps
-    type:
-      - int
-      - 'null'
-  - id: runblastp.taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastp.negative_taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastp.lcase_masking
-    default: false
-    type: boolean
-  - id: runblastn.max_target_seqs
-    default: 100
-    type: int
-  - id: runblastn.word_size
-    default: 28
-    type: int
-  - id: runblastn.reward
-    default: 1
-    type: int
-  - id: runblastn.penalty
-    default: -2
-    type: int
-  - id: runblastn.strand
-    default: both
-    type: string
-  - id: runblastn.gapopen
-    default: 0
-    type: int
-  - id: runblastn.gapextend
-    default: 0
-    type: int
-  - id: runblastn.dust
-    default: "'20 64 1'"
-    type: string
-  - id: runblastn.max_hsps
-    type:
-      - int
-      - 'null'
-  - id: runblastn.tasks
-    default: megablast
-    type: string
-  - id: runblastn.taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastn.negative_taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastn.lcase_masking
-    default: false
-    type: boolean
-  - id: runblastx.max_target_seqs
-    default: 100
-    type: int
-  - id: runblastx.word_size
-    default: 6
-    type: int
-  - id: runblastx.seg
-    default: "'12 2.2 2.5'"
-    type: string
-  - id: runblastx.comp_based_stats
-    default: '2'
-    type: string
-  - id: runblastx.matrix
-    default: BLOSUM62
-    type: string
-  - id: runblastx.gapopen
-    default: 11
-    type: int
-  - id: runblastx.gapextend
-    default: 1
-    type: int
-  - id: runblastx.taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastx.negative_taxids
-    type:
-      - string
-      - 'null'
-  - id: runblastx.max_hsps
-    type:
-      - int
-      - 'null'
-  - id: runblastx.lcase_masking
-    default: false
-    type: boolean
-  - id: runtblastn.max_target_seqs
-    default: 100
-    type: int
-  - id: runtblastn.word_size
-    default: 6
-    type: int
-  - id: runtblastn.seg
-    default: "'12 2.2 2.5'"
-    type: string
-  - id: runtblastn.comp_based_stats
-    default: '2'
-    type: string
-  - id: runtblastn.matrix
-    default: BLOSUM62
-    type: string
-  - id: runtblastn.gapopen
-    default: 11
-    type: int
-  - id: runtblastn.gapextend
-    default: 1
-    type: int
-  - id: runtblastn.lcase_masking
-    default: false
-    type: boolean
-  - id: runtblastn.max_hsps
-    type:
-      - int
-      - 'null'
-  - id: runtblastn.taxids
-    type:
-      - string
-      - 'null'
-  - id: runtblastn.negative_taxids
-    type:
-      - string
-      - 'null'
-  - id: runtblastx.taxids
-    type:
-      - string
-      - 'null'
-  - id: runtblastx.word_size
-    default: 3
-    type: int
-  - id: runtblastx.max_target_seqs
-    default: 100
-    type: int
-  - id: runtblastx.seg
-    default: "'12 2.2 2.5'"
-    type: string
-  - id: runtblastx.matrix
-    default: BLOSUM62
-    type: string
-  - id: runtblastx.lcase_masking
-    default: false
-    type: boolean
-  - id: runtblastx.negative_taxids
-    type:
-      - string
-      - 'null'
-  - id: runtblastx.max_hsps
-    type:
-      - int
-      - 'null'
-steps: []
-outputs:
-  - id: blast.fina_output
-    outputSource: '$([inputs["runtblastx.out"] === null '
-    type: File
+$graph:
+- class: Workflow
+  id: main
+  inputs:
+    - id: blast_docker_override
+      type:
+        - string
+        - 'null'
+    - id: blast_docker
+      type: string
+      # TODO: how to translate the original?
+      #       String blast_docker = select_first([blast_docker_override,"swr.cn-south-1.myhuaweicloud.com/cngbdb/blast:1.2"])
+    - id: queryfa
+      type: File
+    - id: fname
+      type: string
+      default: '/sfs/blastdb/2019_ncov/nucl/v6/ncov'
+    - id: method
+      type: string
+      default: 'blastn'
+    - id: outfmt
+      type: int
+      default: 7
+    - id: evalue
+      type: float
+      default: 10
+    # TODO: how to translate the original?
+    #       String Outfile = basename(queryfa)+'.blast_result.txt'
+    - id: Outfile
+      type: string
+    # runblastn task inputs, to be linked from workflow -> tool
+    - id: runblastn.docker
+      type: string
+    - id: runblastn.Queryfa
+      type: File
+    - id: runblastn.Fname
+      type: string
+    - id: runblastn.max_target_seqs
+      default: 100
+      type: int
+    - id: runblastn.word_size
+      default: 28
+      type: int
+    - id: runblastn.reward
+      default: 1
+      type: int
+    - id: runblastn.penalty
+      default: -2
+      type: int
+    - id: runblastn.strand
+      default: both
+      type: string
+    - id: runblastn.gapopen
+      default: 0
+      type: int
+    - id: runblastn.gapextend
+      default: 0
+      type: int
+    - id: runblastn.dust
+      default: "'20 64 1'"
+      type: string
+    - id: runblastn.max_hsps
+      type:
+        - int
+        - 'null'
+    - id: runblastn.tasks
+      default: megablast
+      type: string
+    - id: runblastn.taxids
+      type:
+        - string
+        - 'null'
+    - id: runblastn.negative_taxids
+      type:
+        - string
+        - 'null'
+    - id: runblastn.lcase_masking
+      default: false
+      type: boolean
+    # runblastp task inputs, to be linked from workflow -> tool
+    - id: runblastp.docker
+      type: string
+    - id: runblastp.Queryfa
+      type: File
+    - id: runblastp.Fname
+      type: string
+    - id: runblastp.max_target_seqs
+      default: 100
+      type: int
+    - id: runblastp.word_size
+      default: 6
+      type: int
+    - id: runblastp.seg
+      default: no
+      type: string
+    - id: runblastp.comp_based_stats
+      default: '2'
+      type: string
+    - id: runblastp.matrix
+      default: BLOSUM62
+      type: string
+    - id: runblastp.gapopen
+      default: 11
+      type: int
+    - id: runblastp.gapextend
+      default: 1
+      type: int
+    - id: runblastp.max_hsps
+      type:
+        - int
+        - 'null'
+    - id: runblastp.taxids
+      type:
+        - string
+        - 'null'
+    - id: runblastp.negative_taxids
+      type:
+        - string
+        - 'null'
+    - id: runblastp.lcase_masking
+      default: false
+      type: boolean
+  steps:
+    - id: runblastp
+      in:
+        Fname: fname
+        Queryfa: queryfa
+        docker: blast_docker
+        outfmt: outfmt
+        Outfile: Outfile
+        threads: threads
+      run: runblastp
+      when: $(inputs.method == 'blastp')
+      out: [out]
+    - id: runblastn
+      in:
+        Fname: fname
+        Queryfa: queryfa
+        docker: blast_docker
+        outfmt: outfmt
+        evalue: evalue
+        Outfile: Outfile
+        threads: threads
+      run: runblastn
+      when: $(inputs.method == 'blastn')
+      out: [out]
+  outputs:
+    - id: fina_output
+      type: File
+      outputSource:
+        - runblastp/out
+        - runblastn/out
+      pickValue: first_non_null
+
+- class: CommandLineTool
+  id: runblastn
+  requirements:
+    - class: InitialWorkDirRequirement
+      listing:
+        - entryname: script.bash
+          entry: |4
+              set -e
+              blastn -db "$(inputs.Fname)" \
+              -show_gis \
+              -query $(inputs.QueryFa) \
+              -outfmt $(inputs.outfmt) \
+              -out     $(inputs.Outfile) \
+              -max_target_seqs $(inputs.max_target_seqs) \
+              -evalue $(inputs.evalue) \
+              -word_size $(inputs.word_size) \
+              -penalty $(inputs.penalty) \
+              -reward  $(inputs.reward) \
+              -dust $(inputs.dust) \
+              -gapopen $(inputs.gapopen) \
+              -gapextend $(inputs.gapextend) \
+              -task $(inputs.tasks) \
+              -strand  $(inputs.strand) \
+              -num_threads $(inputs.threads) \
+              $(true='-lcase_masking' false='' inputs.lcase_masking) $("-max_hsps "+ inputs.max_hsps) $("-taxids " +inputs.taxids) $("-negative_taxids " +inputs.negative_taxids)\
+  hints:
+    - class: DockerRequirement
+    - class: ResourceRequirement
+      coresMin: 8
+      ramMin: 16384
+  inputs:
+    - id: docker
+      type: string
+    - id: Queryfa
+      type: File
+    - id: Fname
+      type: string
+    - id: Outfile
+      type: string
+    - id: threads
+      type: int
+    - id: outfmt
+      type: int
+    - id: max_target_seqs
+      default: 100
+      type: int
+    - id: word_size
+      default: 28
+      type: int
+    - id: reward
+      default: 1
+      type: int
+    - id: penalty
+      default: -2
+      type: int
+    - id: strand
+      default: both
+      type: string
+    - id: gapopen
+      default: 0
+      type: int
+    - id: gapextend
+      default: 0
+      type: int
+    - id: dust
+      default: "'20 64 1'"
+      type: string
+    - id: max_hsps
+      type:
+        - int
+        - 'null'
+    - id: tasks
+      default: megablast
+      type: string
+    - id: taxids
+      type:
+        - string
+        - 'null'
+    - id: negative_taxids
+      type:
+        - string
+        - 'null'
+    - id: lcase_masking
+      default: false
+      type: boolean
+  baseCommand:
+    - bash
+    - script.bash
+  outputs:
+    - id: out
+      type: File
+      outputBinding:
+        glob: $(inputs.Outfile)
+
+- class: CommandLineTool
+  id: runblastp
+  requirements:
+    - class: InitialWorkDirRequirement
+      listing:
+        - entryname: script.bash
+          entry: |4
+              set -e
+              blastp -db "$(inputs.Fname)" \
+              -query $(inputs.Queryfa) \
+              -outfmt $(inputs.outfmt) \
+              -out     $(inputs.Outfile) \
+              -max_target_seqs $(inputs.max_target_seqs) \
+              -comp_based_stats $(inputs.comp_based_stats) \
+              -evalue $(inputs.evalue) \
+              -word_size $(inputs.word_size) \
+              -matrix   $(inputs.matrix) \
+              -seg     $(inputs.seg) \
+              -gapopen $(inputs.gapopen) \
+              -gapextend $(inputs.gapextend) \
+              -num_threads $(inputs.threads) \
+              $(true='-lcase_masking' false='' inputs.lcase_masking) $("-max_hsps "+inputs.max_hsps) $("-taxids " +inputs.taxids) $("-negative_taxids " +inputs.negative_taxids) \
+  hints:
+    - class: DockerRequirement
+    - class: ResourceRequirement
+      coresMin: 8
+      ramMin: 16384
+  inputs:
+    - id: docker
+      type: string
+    - id: Queryfa
+      type: File
+    - id: Fname
+      type: string
+    - id: outfmt
+      type: string
+    - id: Outfile
+      type: string
+    - id: evalue
+      type: float
+    - id: threads
+      type: int
+    - id: max_target_seqs
+      default: 100
+      type: int
+    - id: word_size
+      default: 6
+      type: int
+    - id: seg
+      default: no
+      type: string
+    - id: comp_based_stats
+      default: '2'
+      type: string
+    - id: matrix
+      default: BLOSUM62
+      type: string
+    - id: gapopen
+      default: 11
+      type: int
+    - id: gapextend
+      default: 1
+      type: int
+    - id: max_hsps
+      type:
+        - int
+        - 'null'
+    - id: taxids
+      type:
+        - string
+        - 'null'
+    - id: negative_taxids
+      type:
+        - string
+        - 'null'
+    - id: lcase_masking
+      default: false
+      type: boolean
+  baseCommand:
+    - bash
+    - script.bash
+  outputs:
+    - id: out
+      type: File
+      outputBinding:
+        glob: $(inputs.Outfile)