From 1a0b862a64d34e57371a66803920ade25f9fec36 Mon Sep 17 00:00:00 2001
From: yonezawa-sora <m224825@hiroshima-u.ac.jp>
Date: Tue, 28 May 2024 02:13:19 +0000
Subject: [PATCH] =?UTF-8?q?Workflow=E3=83=95=E3=82=A1=E3=82=A4=E3=83=AB?=
 =?UTF-8?q?=E8=BF=BD=E5=8A=A0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 zatsu_cwl_bioinformatics/blast2tree.cwl       | 113 ++++++++++++++++++
 .../{ => out}/blastdbcmd_result.fasta         |   0
 .../{ => out}/blastp_result.txt               |   0
 .../{ => out}/blastp_result_id.txt            |   0
 .../{ => out}/clustalo_result.fasta           |   0
 .../{ => out}/fasttree_result.nwk             |   0
 6 files changed, 113 insertions(+)
 rename zatsu_cwl_bioinformatics/{ => out}/blastdbcmd_result.fasta (100%)
 rename zatsu_cwl_bioinformatics/{ => out}/blastp_result.txt (100%)
 rename zatsu_cwl_bioinformatics/{ => out}/blastp_result_id.txt (100%)
 rename zatsu_cwl_bioinformatics/{ => out}/clustalo_result.fasta (100%)
 rename zatsu_cwl_bioinformatics/{ => out}/fasttree_result.nwk (100%)

diff --git a/zatsu_cwl_bioinformatics/blast2tree.cwl b/zatsu_cwl_bioinformatics/blast2tree.cwl
index e763050..56b4a68 100644
--- a/zatsu_cwl_bioinformatics/blast2tree.cwl
+++ b/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
+
+      
+
+    
+    
 
diff --git a/zatsu_cwl_bioinformatics/blastdbcmd_result.fasta b/zatsu_cwl_bioinformatics/out/blastdbcmd_result.fasta
similarity index 100%
rename from zatsu_cwl_bioinformatics/blastdbcmd_result.fasta
rename to zatsu_cwl_bioinformatics/out/blastdbcmd_result.fasta
diff --git a/zatsu_cwl_bioinformatics/blastp_result.txt b/zatsu_cwl_bioinformatics/out/blastp_result.txt
similarity index 100%
rename from zatsu_cwl_bioinformatics/blastp_result.txt
rename to zatsu_cwl_bioinformatics/out/blastp_result.txt
diff --git a/zatsu_cwl_bioinformatics/blastp_result_id.txt b/zatsu_cwl_bioinformatics/out/blastp_result_id.txt
similarity index 100%
rename from zatsu_cwl_bioinformatics/blastp_result_id.txt
rename to zatsu_cwl_bioinformatics/out/blastp_result_id.txt
diff --git a/zatsu_cwl_bioinformatics/clustalo_result.fasta b/zatsu_cwl_bioinformatics/out/clustalo_result.fasta
similarity index 100%
rename from zatsu_cwl_bioinformatics/clustalo_result.fasta
rename to zatsu_cwl_bioinformatics/out/clustalo_result.fasta
diff --git a/zatsu_cwl_bioinformatics/fasttree_result.nwk b/zatsu_cwl_bioinformatics/out/fasttree_result.nwk
similarity index 100%
rename from zatsu_cwl_bioinformatics/fasttree_result.nwk
rename to zatsu_cwl_bioinformatics/out/fasttree_result.nwk