diff --git a/.cwl/cwl-metadata-checklist.md b/.cwl/cwl-metadata-checklist.md
new file mode 100644
index 0000000000000000000000000000000000000000..e7b070fda32343db9a484e0c39b84c3c0e484f58
--- /dev/null
+++ b/.cwl/cwl-metadata-checklist.md
@@ -0,0 +1,80 @@
+
+# Checklist for good CWL documents
+
+based on recommendations from:
+
+- https://www.commonwl.org/user_guide/topics/best-practices.html
+- https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html
+
+- [Design](#design)
+ - [Single-step first](#single-step-first)
+- [Dependencies](#dependencies)
+ - [Soft requirements = `hints`](#soft-requirements--hints)
+ - [Hard requirements = `requirements`](#hard-requirements--requirements)
+- [Metadata](#metadata)
+ - [Namespaces and schemas](#namespaces-and-schemas)
+
+## Design
+
+### Keep it Simple: Single-step
+
+- follow the [KISS principle](https://en.wikipedia.org/wiki/KISS_principle)
+- a `CommandLineTool` document should only execute one process
+- use `Workflow` documents to design more complex, multi-step pipelines
+- use `scatter` to execute the process on multiple inputs
+- do not hard code input, output paths
+
+## Dependencies
+
+### Soft requirements = `hints`
+
+Specify software and resource requirements under `hints`
+
+- add `SoftwareRequirement` to specify software version and reference
+ - `package: ` name of the software or package
+ - `specs: ` reference url from https://identifiers.org/biotools/ or SciCrunch https://identifiers.org/rrid/
+ - `version: [ "0.11.9" ]`
+- add `DockerRequirement`
+ - reference a local `Dockerfile` or a published Docker image
+- add `ResourceRequirement` to specify the required compute resources
+
+### Hard requirements = `requirements`
+
+Use the `requirements` primarily to specify hard requirements needed to run the current `CommandLineTool` or `Workflow` document
+
+## Metadata
+
+### Namespaces and schemas
+
+Adding namespaces and schemas allows to reuse them elsewhere in a CWL document
+
+```yaml
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+```
+
+### Attribute authors and contributors
+
+```yaml
+s:author:
+ - class: s:Person
+ s:identifier: <author ORCID>
+ s:email: mailto:<author email>
+ s:name: <author name>
+
+s:contributor:
+ - class: s:Person
+ s:identifier: <contributor ORCID>
+ s:email: mailto:<contributor email>
+ s:name: <contributor name>
+
+s:citation: <DOI to software paper>
+s:codeRepository: <URL to software repo (e.g. github)>
+s:dateCreated: "2016-12-13"
+s:license: <URL to license, e.g. from https://spdx.org/licenses/>
+```
diff --git a/runs/deseq2/run.cwl b/runs/deseq2/run.cwl
index 849cd989221e74fb6874efe6cc412166927a1847..e0fdbf42ee4d373eae50a4e3ccf8fc91ac7229ec 100644
--- a/runs/deseq2/run.cwl
+++ b/runs/deseq2/run.cwl
@@ -22,3 +22,16 @@ outputs:
output:
type: File[]
outputSource: deseq2/output
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/runs/fastqc/run.cwl b/runs/fastqc/run.cwl
index b049a5f92ccca308657a8791af4c5d52f3871da3..fb4552b550fe0896cb4d170b5b3e17a6b286d5e4 100644
--- a/runs/fastqc/run.cwl
+++ b/runs/fastqc/run.cwl
@@ -21,4 +21,17 @@ steps:
outputs:
fastqc_outdir:
type: Directory
- outputSource: fastqc/fastqc_outdir
\ No newline at end of file
+ outputSource: fastqc/fastqc_outdir
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/runs/isaSampleToRawDataSeq/run.cwl b/runs/isaSampleToRawDataSeq/run.cwl
index aca29e7543721a02e4a3a7eee0650b1167615a0f..803f5317df681038d9edd21271dd72e34ed82b32 100644
--- a/runs/isaSampleToRawDataSeq/run.cwl
+++ b/runs/isaSampleToRawDataSeq/run.cwl
@@ -25,4 +25,17 @@ outputs:
outputSource: isaSampleToRawDataSeq/sampleseqCsv
sampleseqXlsx:
type: File
- outputSource: isaSampleToRawDataSeq/sampleseqXlsx
\ No newline at end of file
+ outputSource: isaSampleToRawDataSeq/sampleseqXlsx
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/runs/kallisto/run.cwl b/runs/kallisto/run.cwl
index d702ed4426bff5a1890b4f9f0ce0de6acb1743c8..f06fae261e1b544c9e69ca475b8100a15f9f0ec9 100644
--- a/runs/kallisto/run.cwl
+++ b/runs/kallisto/run.cwl
@@ -41,3 +41,16 @@ outputs:
kallistoOutDir:
type: Directory
outputSource: kallisto/kallistoOutDir
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/runs/shiny/run.cwl b/runs/shiny/run.cwl
index 71435f9c300a86f8781e80fa0e7b6b927e8c9da0..532fa889f33f0683fd4dcc4be9bc140ba815571a 100644
--- a/runs/shiny/run.cwl
+++ b/runs/shiny/run.cwl
@@ -16,3 +16,16 @@ steps:
out: []
outputs: []
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
diff --git a/runs/sleuth/run.cwl b/runs/sleuth/run.cwl
index e00ce51a124f5266ae6f383ba5d21ba4383ffc57..7884d8dcbd318257bfaf4de6ef0a93b603875cbb 100644
--- a/runs/sleuth/run.cwl
+++ b/runs/sleuth/run.cwl
@@ -27,3 +27,17 @@ outputs:
outdir:
type: Directory[]
outputSource: sleuth/outdir
+
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/workflows/fastqc/fastqc.cwl b/workflows/fastqc/fastqc.cwl
index 1954ad092600ec32cd7074488ff8d1111fe142de..4f96fb6ee286f9c022671e00dbdaa04a686f98dc 100644
--- a/workflows/fastqc/fastqc.cwl
+++ b/workflows/fastqc/fastqc.cwl
@@ -19,10 +19,10 @@ hints:
dockerPull: quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1
SoftwareRequirement:
packages:
- fastqc:
+ - package: fastqc
specs:
- https://identifiers.org/biotools/fastqc
- - - https://identifiers.org/rrid/RRID:SCR_014583
+ - https://identifiers.org/rrid/RRID:SCR_014583
version: [ "0.11.9" ]
baseCommand: "fastqc"
@@ -58,5 +58,3 @@ $schemas:
- https://edamontology.org/EDAM_1.25.owl
s:license: https://spdx.org/licenses/GPL-3.0-or-later
-
-
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 10f879d61317f9d5f3dfc52f7bef054b9bb3c250..1a4b3c96e3a9b20f201c687f148ab94513f8792c 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -33,7 +33,7 @@ hints:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
- kallisto:
+ - package: kallisto
version: [ "0.51.1" ]
specs:
- https://identifiers.org/rrid/RRID:SCR_016582
@@ -82,5 +82,8 @@ $namespaces:
s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.25.owl
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
s:license: https://spdx.org/licenses/BSD-2-Clause
+s:citation: https://dx.doi.org/10.1038/nbt.3519
+s:codeRepository: https://github.com/pachterlab/kallisto
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 1a8e6eaa87bbcc8a921d40416092d3768ad5ced5..93ff361284fa411c945fcbb5ddf4c498770160f8 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -45,7 +45,7 @@ hints:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
- kallisto:
+ - package: kallisto
version: [ "0.51.1" ]
specs: [ https://identifiers.org/biotools/kallisto ]
@@ -175,5 +175,8 @@ $namespaces:
s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.25.owl
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
s:license: https://spdx.org/licenses/BSD-2-Clause
+s:citation: https://dx.doi.org/10.1038/nbt.3519
+s:codeRepository: https://github.com/pachterlab/kallisto