Merge pull request #21 from broadinstitute/CleanUp

Clean up this repo.
broadinstitute · Mar 6, 2023 · 0c3e2a5 · 0c3e2a5
2 parents 28f9e18 + 405efd8
commit 0c3e2a5
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Showing 28 changed files with 25 additions and 3,379 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -1,25 +1,10 @@
 version: 1.2
 workflows:
- - name: SS2_scRNA_pipeline
-   subclass: WDL
-   primaryDescriptorPath: /wdl/SS2_scRNA_pipeline.wdl
-   testParameterFiles:
-   - /input_json/ss2_scRNA_pipeline_inputs.json
- - name: SC_Plate_QC
-   subclass: WDL
-   primaryDescriptorPath: /wdl/SC_Plate_QC.wdl
-   testParameterFiles:
-   - /input_json/SC_Plate_QC_pipeline_inputs.json
- - name: CramToBam
-   subclass: WDL
-   primaryDescriptorPath: /wdl/CramToBam.wdl
-   testParameterFiles:
-   - /input_json/CramToBam_inputs.json
  - name: CollectSamErrorMetrics
    subclass: WDL
-   primaryDescriptorPath: /wdl/CollectSamErrorMetrics.wdl
+   primaryDescriptorPath: /CollectSamError/CollectSamErrorMetrics.wdl
    testParameterFiles:
-   - /input_json/CollectSamErrorMetrics_inputs.json
+   - /CollectSamError/CollectSamErrorMetrics.inputs.json
  - name: BenchmarkCNV
    subclass: WDL
    primaryDescriptorPath: /BenchmarkCNV/BenchmarkCNV.wdl

diff --git a/CollectSamError/CollectSamErrorMetrics.inputs.json b/CollectSamError/CollectSamErrorMetrics.inputs.json
@@ -0,0 +1,12 @@
+{
+    "CollectSamErrorMetrics.CollectSamErrorMetricsTask.disk_gb": "${}",
+    "CollectSamErrorMetrics.CollectSamErrorMetricsTask.memory_gb": "${}",
+    "CollectSamErrorMetrics.input_bam": "${this.bam_file}",
+    "CollectSamErrorMetrics.intervals": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
+    "CollectSamErrorMetrics.output_name": "${this.sample_id}",
+    "CollectSamErrorMetrics.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+    "CollectSamErrorMetrics.ref_fai": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
+    "CollectSamErrorMetrics.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
+    "CollectSamErrorMetrics.vcf_file": "gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz",
+    "CollectSamErrorMetrics.vcf_index_file": "gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi"
+}
diff --git a/wdl/CollectSamErrorMetrics.wdl → CollectSamError/CollectSamErrorMetrics.wdl b/wdl/CollectSamErrorMetrics.wdl → CollectSamError/CollectSamErrorMetrics.wdl
@@ -63,5 +63,4 @@ task CollectSamErrorMetricsTask {
         memory: memory_gb + "GB"
         cpu: "1"
     }
-}
-
+}
diff --git a/README.md b/README.md
@@ -1,24 +1,13 @@
-# Translational Analysis Group (TAG) Public Repo
+# Translational Analysis Group (TAG) Workflow Repository
 
-This github repository contains public Terra workflows maintained by
-Translational Analysis Group (TAG). Below is the workflows TAG published.
+This is Translational Analysis Group (TAG) public repository, where we maintain frequently 
+used utility workflows for the team. Our goal is to facilitate their use on Terra through 
+Dockstore, allowing for easy access and streamlined usage.
 
-## SmartSeq QC
-A pipeline for quality control of Smart Seq single cell analysis:
-* SS2_scRNA_pipeline
-* SC_Plate_QC
+**NOTE: this Repo is public, so anything you add to this repo is viewable by anyone.**
 
-## ichorCNA 
-A workflow that estimates tumor purity and ploidy of blood samples using ultra-low pass (ULP) whole-genome sequencing 
-(WGS) technology. 
-* ichorCNA_step1
-* ichorCNA_step2
-
-## CramToBam
-A workflow for converting CRAM file to BAM file.
-
-## CollectSamErrorMetrics
-A workflow for collecting error metrics from alignment file.
-
-## BenchmarkCNV
-A workflow for benchmarking copy number variation detection algorithms.
+## Using the Dockstore Automatically Update Workflows in Terra
+Workflows registered in Dockstore can be automatically synced when changes are pushed 
+to this repo by adding their information to `.dockstore.yml`. This allows any updates or 
+changes made to a workflow in this repo to be immediately reflected in any Terra workspaces 
+using that workflow. 
diff --git a/input_json/.DS_Store b/input_json/.DS_Store
diff --git a/input_json/CollectSamErrorMetrics_inputs.json b/input_json/CollectSamErrorMetrics_inputs.json
diff --git a/input_json/CramToBam_inputs.json b/input_json/CramToBam_inputs.json
diff --git a/input_json/README.md b/input_json/README.md
diff --git a/input_json/SC_Plate_QC_pipeline_inputs.json b/input_json/SC_Plate_QC_pipeline_inputs.json
diff --git a/input_json/cnv_somatic_pair_workflow_inputs.json b/input_json/cnv_somatic_pair_workflow_inputs.json
diff --git a/input_json/ichorCNA_step1_pipeline_inputs.json b/input_json/ichorCNA_step1_pipeline_inputs.json
diff --git a/input_json/ichorCNA_step1_pipeline_outputs.json b/input_json/ichorCNA_step1_pipeline_outputs.json
diff --git a/input_json/ichorCNA_step2_pipeline_inputs.json b/input_json/ichorCNA_step2_pipeline_inputs.json
diff --git a/input_json/ichorCNA_step2_pipeline_outputs.json b/input_json/ichorCNA_step2_pipeline_outputs.json
diff --git a/input_json/ss2_scRNA_pipeline_inputs.json b/input_json/ss2_scRNA_pipeline_inputs.json
diff --git a/wdl/.DS_Store b/wdl/.DS_Store
diff --git a/wdl/CramToBam.wdl b/wdl/CramToBam.wdl
diff --git a/wdl/README.md b/wdl/README.md
-Original file line number
+Diff line change
@@ Expand Up / @@ -63,5 +63,4 @@ task CollectSamErrorMetricsTask { @@
             memory: memory_gb + "GB"
             cpu: "1"
         }
-    }
+    }