align with spec: kallisto

runs/kallisto/README.md

-# Kallisto Workflow
-
-## Executing the multi-step workflow
-
-```bash
-cd runs/kallisto/
-cwltool --cachedir cache2 ../../workflows/kallisto/kallisto-workflow.cwl workflow.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
-```

runs/kallisto/run.cwl

+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  SubworkflowFeatureRequirement: {}
+
+inputs:
+  IndexInput: File[]
+  InputReadsMultipleSamples:
+    type: 
+      type: array
+      items: 
+        type: array
+        items: File
+  numUnderscoresFileName: int
+  isSingle: boolean
+  FragmentLength: double?  
+  StandardDeviation: double?
+  BootstrapSamples: int?
+  resultsFolder: string
+
+steps:
+  kallisto:
+    run:  ../../workflows/kallisto/workflow.cwl
+    in:
+      IndexInput: IndexInput
+      InputReadsMultipleSamples: InputReadsMultipleSamples
+      numUnderscoresFileName: numUnderscoresFileName
+      isSingle: isSingle
+      FragmentLength: FragmentLength
+      StandardDeviation: StandardDeviation
+      BootstrapSamples: BootstrapSamples
+      resultsFolder: resultsFolder
+    out: [finalOut]
+
+outputs:
+  finalOut:
+    type: Directory[]
+    outputSource: kallisto/finalOut

runs/kallisto/workflow.yml → runs/kallisto/run.yml

@@ -17,22 +17,22 @@ InputReadsMultipleSamples:
     - class: File
       path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
       format: edam:format_1930 # FASTQ
-  - 
-    - class: File
-      path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
-      format: edam:format_1930 # FASTQ
-  - 
-    - class: File
-      path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
-      format: edam:format_1930 # FASTQ
-  - 
-    - class: File
-      path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
-      format: edam:format_1930 # FASTQ
-  - 
-    - class: File
-      path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
-      format: edam:format_1930 # FASTQ
+  # - 
+  #   - class: File
+  #     path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+  #     format: edam:format_1930 # FASTQ
+  # - 
+  #   - class: File
+  #     path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+  #     format: edam:format_1930 # FASTQ
+  # - 
+  #   - class: File
+  #     path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+  #     format: edam:format_1930 # FASTQ
+  # - 
+  #   - class: File
+  #     path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+  #     format: edam:format_1930 # FASTQ
 
 numUnderscoresFileName: 2
 
@@ -42,7 +42,7 @@ FragmentLength: 200
 StandardDeviation: 20
 BootstrapSamples: 30
 
-resultsFolder: kallisto_results
+resultsFolder: test
 
 $namespaces:
   edam: https://edamontology.org/
\ No newline at end of file

workflows/kallisto/kallisto-index.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
+    dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
   SoftwareRequirement:
     packages:
       kallisto:

workflows/kallisto/kallisto-quant.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
+    dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
   SoftwareRequirement:
     packages:
       kallisto: