diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md index 644698a127f0834a44725ff204d65cbcd39b1461..08cf2285fde86af02d22aee4681882eb2f1202e0 100644 --- a/runs/kallisto_collect/README.md +++ b/runs/kallisto_collect/README.md @@ -9,5 +9,5 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto ```bash ### run with cwltool -cwltool --enable-dev run.cwl kallisto_collect.yml +cwltool run.cwl kallisto_collect.yml ``` diff --git a/runs/kallisto_collect/run.cwl b/runs/kallisto_collect/run.cwl index 3bd1e3722ae74e396574bd94ff033347d5711554..2736cc493acbad35870977c85eea6daec7a92edc 100644 --- a/runs/kallisto_collect/run.cwl +++ b/runs/kallisto_collect/run.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: Workflow inputs: in_kallisto_results: diff --git a/runs/kallisto_index/README.md b/runs/kallisto_index/README.md index 2271f59ce8011456c57cf35c81eb0d954ffc30fa..ac67bff2d660c23469c2aa366693a9f42c3e7825 100644 --- a/runs/kallisto_index/README.md +++ b/runs/kallisto_index/README.md @@ -9,5 +9,5 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto ```bash ### run with cwltool -cwltool --enable-dev run.cwl kallisto_index.yml +cwltool run.cwl kallisto_index.yml ``` diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl index 848b96d69b73dcd198332e1049d019633ef5c8c8..a115ab7926f4c454ce8b95bc642571030b957066 100644 --- a/runs/kallisto_index/run.cwl +++ b/runs/kallisto_index/run.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: Workflow inputs: in_genome_ref: diff --git a/runs/kallisto_quant/README.md b/runs/kallisto_quant/README.md index b3a3ac8bffaa087680fe1d6996d2088ccc2e3e90..86c10cd181b91cefc59660d5f030a5a9db80cb98 100644 --- a/runs/kallisto_quant/README.md +++ b/runs/kallisto_quant/README.md @@ -9,5 +9,5 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto ```bash ### run with cwltool -cwltool --enable-dev run.cwl kallisto_quant.yml +cwltool run.cwl kallisto_quant.yml ``` diff --git a/runs/kallisto_quant/run.cwl b/runs/kallisto_quant/run.cwl index 87cc30fd0557a67aff2ec890055e8513472f5d22..af2bc99c83d6ae8a2c0db7775ce28f5cb009ecbd 100644 --- a/runs/kallisto_quant/run.cwl +++ b/runs/kallisto_quant/run.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: Workflow inputs: out_folder: diff --git a/runs/kallisto_sleuth/README.md b/runs/kallisto_sleuth/README.md index ade0a1e2685107ad77dd88382d2f7c7f57fef203..8fc55827f0968cd26b3f30105bad7eeed2767ba2 100644 --- a/runs/kallisto_sleuth/README.md +++ b/runs/kallisto_sleuth/README.md @@ -9,5 +9,5 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto ```bash ### run with cwltool -cwltool --enable-dev run.cwl kallisto_sleuth.yml +cwltool run.cwl kallisto_sleuth.yml ``` diff --git a/runs/kallisto_sleuth/run.cwl b/runs/kallisto_sleuth/run.cwl index 803541479d960daaf3984d6d9c9b0abe52f9845e..dc8b77af8941b3988530ec0fa5c4ed74d52b0420 100644 --- a/runs/kallisto_sleuth/run.cwl +++ b/runs/kallisto_sleuth/run.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: Workflow inputs: in_sleuth: diff --git a/runs/shiny_prep/README.md b/runs/shiny_prep/README.md index d27503bc3cc01d16bdb4802d6c6ee5d8e461d958..75aee01b7b5f1cf1971623c801979d0378299019 100644 --- a/runs/shiny_prep/README.md +++ b/runs/shiny_prep/README.md @@ -9,5 +9,5 @@ cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto ```bash ### run with cwltool -cwltool --enable-dev run.cwl shiny_prep.yml +cwltool run.cwl shiny_prep.yml ``` diff --git a/runs/shiny_prep/run.cwl b/runs/shiny_prep/run.cwl index 13e324a958e89a75f567c5f3e9f6634de3b5442a..4f5b2adc81b5e022925d3e753a1531d528e867a1 100644 --- a/runs/shiny_prep/run.cwl +++ b/runs/shiny_prep/run.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: Workflow inputs: out_folder: diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl index a109fb0cb1d33cd5bfec67554e041adaa35ffd09..b5ed0f7fe34a6a740b6986efc079473186ad0c11 100644 --- a/workflows/kallisto_collect/workflow.cwl +++ b/workflows/kallisto_collect/workflow.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/workflows/kallisto_index/workflow.cwl b/workflows/kallisto_index/workflow.cwl index f102e5c50562326df26659eb7f68da73d2504808..32635f746d02b1061a0fe8d020045d2afe93b399 100644 --- a/workflows/kallisto_index/workflow.cwl +++ b/workflows/kallisto_index/workflow.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/workflows/kallisto_quant/workflow.cwl b/workflows/kallisto_quant/workflow.cwl index 90aa9da3b9c65c9330edeb1c1f2b5a8d6bdb5b71..1041d7325d1c14ee4b634da642844da1a34f1ea8 100644 --- a/workflows/kallisto_quant/workflow.cwl +++ b/workflows/kallisto_quant/workflow.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/workflows/kallisto_sleuth/workflow.cwl b/workflows/kallisto_sleuth/workflow.cwl index ec2800ba2a9a7886f7e522d6db1538563a74b754..48ac0b12fa9b8a22f117d806bc0dd196a3319d35 100644 --- a/workflows/kallisto_sleuth/workflow.cwl +++ b/workflows/kallisto_sleuth/workflow.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/workflows/shiny_prep/workflow.cwl b/workflows/shiny_prep/workflow.cwl index 4caf713393173d1bb20ca034fd2926c1e5301ac3..0e059d4968947b2f925c583b15b17e96d929a02d 100644 --- a/workflows/shiny_prep/workflow.cwl +++ b/workflows/shiny_prep/workflow.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.2.0-dev1 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: