add index file

.gitattributes

@@ -0,0 +1,16 @@
+index/index_swissprot/swissprot.lookup filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_h.index filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_mapping filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ss.index filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot.version filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ss.dbtype filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot.dbtype filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot.index filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ca.index filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_h filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ss filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ca filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_ca.dbtype filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_h.dbtype filter=lfs diff=lfs merge=lfs -text
+index/index_swissprot/swissprot_taxonomy filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+# copy from Tanjo-san's repository https://github.com/tom-tan/cwl-template-for-vscode/blob/main/.github/workflows/ci.yml
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup python for cwltool
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11.x'
+    - name: Install cwltool
+      run: pip install cwltool
+    - uses: actions/setup-node@v4
+      with:
+        node-version: 'latest'
+    - name: Run tests
+      id: run-tests
+      uses: common-workflow-lab/run-tests@v1
+      with:
+        test-list: test.yml
+        runner: cwltool
+        timeout: 30

.gitignore

@@ -1,8 +1,8 @@
 .vscode
 .cache
+/index/index_pdb
 .DS_Store
 /cwl_cache
-/index
 /Data
 /scripts/archive
 /test/oryza_sativa_test/uniprotkb_39947_all.fasta

Tools/02_foldseek_database.cwl

@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-# Generated from: foldseek databases CATH50 cath50 tmp --threads 16
+# Generated from: foldseek databases Alphafold/Swiss-Prot index_swissprot tmp --threads 16
 class: CommandLineTool
 cwlVersion: v1.2
 
@@ -26,7 +26,7 @@ inputs:
 arguments:
   - shellQuote: false
     valueFrom: |
-      mkdir -p $(inputs.index_dir_name) && \
+      mkdir -p $(inputs.index_dir_name)
       foldseek databases $(inputs.database) $(inputs.index_dir_name)/$(inputs.index_name) $(runtime.tmpdir) --threads $(inputs.threads)
 
 outputs:

Tools/02_foldseek_database_cp.cwl

@@ -0,0 +1,47 @@
+#!/usr/bin/env cwl-runner
+# Generated from: foldseek databases CATH50 cath50 tmp --threads 16
+class: CommandLineTool
+cwlVersion: v1.2
+
+requirements:
+  ShellCommandRequirement: {}
+  NetworkAccess:
+    networkAccess: true
+inputs:
+  - id: database
+    label: "Database name"
+    type: string
+    default: "Alphafold/Swiss-Prot"
+  - id: index_dir_name
+    label: "Index directory name"
+    type: string
+    default: "index_swissprot"
+  - id: index_name
+    type: string
+    default: "swissprot"
+  - id: tmp_dir
+    type: string
+    default: "tmp"
+  - id: threads
+    type: int
+    default: 16
+
+arguments:
+  - shellQuote: false
+    valueFrom: |
+      mkdir -p $(inputs.index_dir_name)
+      foldseek databases $(inputs.database) $(inputs.index_dir_name)/$(runtime.tmpdir) $(inputs.tmp_dir) --threads $(inputs.threads)
+
+outputs:
+  - id: all-for-debugging
+    type:
+      type: array
+      items:
+        - File
+        - Directory
+    outputBinding:
+      glob: "*"
+
+hints:
+  - class: DockerRequirement
+    dockerPull: quay.io/biocontainers/foldseek:9.427df8a--pl5321hb365157_1

test.yml

@@ -0,0 +1,10 @@
+- job: job/plant2human_job_example_os.yml #index ファイルを後で別の所に置いておく
+  tool: Workflow/plant2human.cwl
+  output:
+    out:
+      class: File
+      basename: output.txt
+      checksum: sha1$2af1a59da667eb4aedb182248c1d91741df7e24d # このchecksumはどこから取ってくる？？
+      size: 31
+  doc: Template for cwltest
+  id: test-example