Merge pull request #388 from umccr/umccrise_v2.3.1--1

umccrise v2.3.1 tool def

.github/catalogue/docs/tools/umccrise/2.3.1--1/umccrise__2.3.1--1.md

@@ -0,0 +1,244 @@
+
+umccrise 2.3.1--1 tool
+======================
+
+## Table of Contents
+
+- [Overview](#umccrise-v231--1-overview)  
+- [Links](#related-links)  
+- [Inputs](#umccrise-v231--1-inputs)  
+- [Outputs](#umccrise-v231--1-outputs)  
+- [ICA](#ica)  
+
+
+## umccrise v(2.3.1--1) Overview
+
+
+
+
+> ID: umccrise--2.3.1--1  
+> md5sum: 6cbf94c19b9e73fbdf33ee3300980d70
+
+### umccrise v(2.3.1--1) documentation
+
+Documentation for umccrise v2.3.1--1
+
+### Categories
+
+
+
+## Related Links
+
+- [CWL File Path](../../../../../../tools/umccrise/2.3.1--1/umccrise__2.3.1--1.cwl)  
+
+
+
+
+## umccrise v(2.3.1--1) Inputs
+
+### debug
+
+
+
+
+> ID: debug
+  
+**Optional:** `True`  
+**Type:** `boolean`  
+**Docs:**  
+Copy workspace to output directory if workflow fails
+
+
+### dragen germline directory
+
+
+
+
+> ID: dragen_germline_directory
+  
+**Optional:** `False`  
+**Type:** `Directory`  
+**Docs:**  
+The dragen germline directory
+
+
+### dragen normal id
+
+
+
+
+> ID: dragen_normal_id
+  
+**Optional:** `True`  
+**Type:** `string`  
+**Docs:**  
+The name of the dragen normal sample
+
+
+### dragen somatic directory
+
+
+
+
+> ID: dragen_somatic_directory
+  
+**Optional:** `False`  
+**Type:** `Directory`  
+**Docs:**  
+The dragen somatic directory
+
+
+### dragen tumor id
+
+
+
+
+> ID: dragen_tumor_id
+  
+**Optional:** `True`  
+**Type:** `string`  
+**Docs:**  
+The name of the dragen tumor sample
+
+
+### dry run
+
+
+
+
+> ID: dry_run
+  
+**Optional:** `True`  
+**Type:** `boolean`  
+**Docs:**  
+Prints rules and commands to be run without actually executing them
+
+
+### genomes tar
+
+
+
+
+> ID: genomes_tar
+  
+**Optional:** `False`  
+**Type:** `File`  
+**Docs:**  
+The reference umccrise tarball
+
+
+### include stage
+
+
+
+
+> ID: include_stage
+  
+**Optional:** `True`  
+**Type:** `.[]`  
+**Docs:**  
+Optionally, specify stage(s) to run
+
+
+### output directory name
+
+
+
+
+> ID: output_directory_name
+  
+**Optional:** `False`  
+**Type:** `string`  
+**Docs:**  
+The name of the output directory
+
+
+### skip stage
+
+
+
+
+> ID: skip_stage
+  
+**Optional:** `True`  
+**Type:** `.[]`  
+**Docs:**  
+Runs all default stage(s) excluding the one selected
+
+
+### subject identifier
+
+
+
+
+> ID: subject_identifier
+  
+**Optional:** `False`  
+**Type:** `string`  
+**Docs:**  
+The subject ID (used to name output files)
+
+
+### threads
+
+
+
+
+> ID: threads
+  
+**Optional:** `True`  
+**Type:** `int`  
+**Docs:**  
+Number of threads to use
+
+
+
+
+## umccrise v(2.3.1--1) Outputs
+
+### output directory
+
+
+
+
+> ID: umccrise--2.3.1--1/output_directory  
+
+
+**Optional:** `False`  
+**Output Type:** `Directory`  
+**Docs:**  
+The output directory containing the umccrise data
+
+
+
+
+
+## ICA
+
+### ToC
+
+- [development_workflows](#project-development_workflows)  
+- [production_workflows](#project-production_workflows)  
+
+
+### Project: development_workflows
+
+
+> wfl id: wfl.af61d2b172e84cbfa85eaf184226db8b  
+
+
+**workflow name:** umccrise_dev-wf  
+**wfl version name:** 2.3.1--1  
+
+
+### Project: production_workflows
+
+
+> wfl id: wfl.714e9172f3674023b210ccc7c47db05a  
+
+
+**workflow name:** umccrise_prod-wf  
+**wfl version name:** 2.3.1--1--9344851  
+
+
+

config/project.yaml

@@ -352,6 +352,11 @@ projects:
             ica_workflow_version_name: 2.3.0--0
             modification_time: 2023-05-15T04:27:57UTC
             run_instances: []
+          - name: 2.3.1--1
+            path: 2.3.1--1/umccrise__2.3.1--1.cwl
+            ica_workflow_version_name: 2.3.1--1
+            modification_time: 2023-09-13T13:24:08UTC
+            run_instances: []
       - name: dragen-somatic
         path: dragen-somatic
         ica_workflow_name: dragen-somatic_dev-wf
@@ -1376,6 +1381,11 @@ projects:
             ica_workflow_version_name: 2.3.0--0--2990cf1
             modification_time: 2023-05-16T05:37:43UTC
             run_instances: []
+          - name: 2.3.1--1
+            path: 2.3.1--1/umccrise__2.3.1--1.cwl
+            ica_workflow_version_name: 2.3.1--1--9344851
+            modification_time: 2023-09-13T23:40:12UTC
+            run_instances: []
     workflows:
       - name: tso500-ctdna
         path: tso500-ctdna

config/tool.yaml

@@ -390,6 +390,9 @@ tools:
       - name: 2.3.0--0
         path: 2.3.0--0/umccrise__2.3.0--0.cwl
         md5sum: ab13fdc5b457f671f1891b8451721466
+      - name: 2.3.1--1
+        path: 2.3.1--1/umccrise__2.3.1--1.cwl
+        md5sum: 6cbf94c19b9e73fbdf33ee3300980d70
     categories: []
   - name: custom-create-umccr-dragen-refdata-tarball-from-illumina-tar
     path: custom-create-umccr-dragen-refdata-tarball-from-illumina-tar

cwl-ica-catalogue.md

@@ -534,6 +534,7 @@ UMCCR CWL-ICA Catalogue
 - [2.2.0--0](.github/catalogue/docs/tools/umccrise/2.2.0--0/umccrise__2.2.0--0.md)  
 - [2.2.1--0](.github/catalogue/docs/tools/umccrise/2.2.1--0/umccrise__2.2.1--0.md)  
 - [2.3.0--0](.github/catalogue/docs/tools/umccrise/2.3.0--0/umccrise__2.3.0--0.md)  
+- [2.3.1--1](.github/catalogue/docs/tools/umccrise/2.3.1--1/umccrise__2.3.1--1.md)  
 
 
 ### custom-create-umccr-dragen-refdata-tarball-from-illumina-tar