Workflowファイル追加

zatsu_cwl_bioinformatics/blast2tree.cwl

@@ -1,4 +1,117 @@
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
+doc: "blastp, awk, blastdbcmd, clustalo, and fasttreeの5つのステップを実行"
+
+inputs:
+  - id: 1_protein_query
+    type: File
+    doc: "blastp process input protein query file(fasta format)"
+    default:
+      class: File
+      location: ./MSTN.fasta
+  - id: 2_protein_database
+    type: File
+    doc: "blastp process input all index file"
+    default:
+      class: File
+      location: ./uniprot_sprot.fasta
+    secondaryFiles:
+      - ^.fasta.phd
+      - ^.fasta.phi
+      - ^.fasta.phr
+      - ^.fasta.pin
+      - ^.fasta.pog
+      - ^.fasta.psd
+      - ^.fasta.psi
+      - ^.fasta.psq
+  - id: 3_evalue
+    type: float
+    doc: "blastp process evalue cutoff"
+    default: 0.01
+  - id: 4_number_of_threads
+    type: int
+    doc: "number of threads"
+    default: 8
+  - id: 5_outformat_type
+    type: int
+    doc: "blastp process output format type"
+    default: 6
+  - id: 6_output_file_name
+    type: string
+    doc: "blastp process output file name"
+    default: blastp_output.txt
+  - id: 7_max_target_sequence
+    type: int
+    doc: "blastp process max target sequence"
+    default: 20
+  - id: 8_blastdbcmd_protein_database
+    type: File
+    doc: "blastdbcmd process protein database"
+    default:
+      class: File
+      location: ./uniprot_sprot.fasta
+    secondaryFiles:
+      - ^.fasta.phd
+      - ^.fasta.phi
+      - ^.fasta.phr
+      - ^.fasta.pin
+      - ^.fasta.pog
+      - ^.fasta.psd
+      - ^.fasta.psi
+      - ^.fasta.psq
+  - id: 10_clustalo_output_name
+    type: string
+    doc: "clustalo process output name"
+    default: clustalo_output.fasta
+
+steps:
+  step1_blastp:
+    run: 1_blastp_docker_v4.cwl
+    in: 
+      query: 1_protein_query
+      db: 2_protein_database
+      evalue: 3_evalue
+      num_threads: 4_number_of_threads
+      outfmt: 5_outformat_type
+      out: 6_output_file_name
+      max_target_seqs: 7_max_target_sequence
+    out: [all-for-debugging]
+
+  step2_awk:
+    run: 2_awk_v2.cwl
+    in:
+      blastp_result: step1_blastp/all-for-debugging
+    out: [out]
+
+  step3_blastdbcmd:
+    run: 3_blastdbcmd_docker_v2.cwl
+    in:
+      db: 8_blastdbcmd_protein_database
+      entry_batch: step2_awk/out
+    out: [all-for-debugging]
+
+  step4_clustalo:
+    run: 4_clustalo_docker.cwl
+    in: 
+      i: step3_blastdbcmd/all-for-debugging
+      o_name: 10_clustalo_output_name
+    out: [all-for-debugging]
+
+  step5_fasttree:
+    run: 5_fasttree_docker.cwl
+    in:
+      nt: step4_clustalo/all-for-debugging
+    out: [out]
+
+outputs:
+  final_output_bootstrap:
+    type: File
+    doc: "final output file"
+    outputSource: step5_fasttree/out
+
+
+
+
+