Merge branch 'master' of git.wur.nl:unlock/cwl

.gitignore

+tests

cwl/kraken2/kraken2-build.cwl

+#!/usr/bin/env cwltool
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+# hints:
+#   SoftwareRequirement:
+#     packages:
+#       kraken2:
+#         version: ["2.1.2"]
+#         specs: ["https://anaconda.org/bioconda/kraken2"]
+
+# baseCommand: [ /unlock/infrastructure/binaries/kraken2-2.0.9-beta/kraken2 ]
+baseCommand: ["bash","-x", "script.sh"]
+
+
+label: "Kraken2 metagenomics read classification"
+doc: |
+    Kraken2 metagenomics read classification.
+    
+    Updated databases available at: https://benlangmead.github.io/aws-indexes/k2 (e.g. PlusPF-8)
+    Original db: https://ccb.jhu.edu/software/kraken2/index.shtml?t=downloads
+
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: "$({class: 'Directory', listing: []})"
+        entryname: "kraken2_output"
+        writable: true
+      - entryname: script.sh
+        entry: |-
+          #!/bin/bash
+          PATH=/unlock/infrastructure/binaries/BLAST/ncbi-blast-2.13.0+/bin/:"$PATH"
+          chmod +x /unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/*
+          DBNAME=KRAKEN2_$1
+          threads=$2
+          /unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/kraken2-build --download-taxonomy --db $DBNAME
+          shift;shift;
+          for file in "$@"
+          do
+              echo "Processing $file";
+              /unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/kraken2-build --add-to-library $file --db $DBNAME
+          done
+          /unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/kraken2-build --threads $threads --build --db $DBNAME
+
+
+inputs:
+  identifier:
+    type: string
+    doc: Identifier for this dataset used in this workflow
+    label: identifier used
+    inputBinding:
+      position: 1
+  threads:
+    type: int?
+    default: 1
+    inputBinding:
+      position: 2
+  references:
+    type: string[]
+    doc: List of genome references for kraken
+    inputBinding:
+      position: 10
+
+outputs:
+  kraken2_database: 
+    type: Directory
+    outputBinding:
+      glob: KRAKEN2_*
+
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0001-8172-8981
+    s:email: mailto:jasper.koehorst@wur.nl
+    s:name: Jasper Koehorst
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0001-9524-5964
+    s:email: mailto:bart.nijsse@wur.nl
+    s:name: Bart Nijsse
+
+s:citation: https://m-unlock.nl
+s:codeRepository: https://gitlab.com/m-unlock/cwl
+s:dateCreated: "2022-01-01"
+s:license: https://spdx.org/licenses/Apache-2.0 
+s:copyrightHolder: "UNLOCK - Unlocking Microbial Potential"
+
+$namespaces:
+  s: https://schema.org/
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