Minor update

README.md

@@ -1,40 +1,35 @@
 # wdl-cellranger-gex
 
-WDLized Cell Ranger Gene Expression
+WDLized Cell Ranger Gene Expression Pipeline
 
 ## Setup
 
-```bash
-aws s3 cp s3://dp-lab-home/software/install-CellRangerGex-6.0.2.sh - | bash
-```
+The pipeline is a part of SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/). For setup, please refer to [this page](https://github.com/hisplan/scing). All the instructions below is given under the assumption that you have already configured SCING in your environment.
 
-```bash
-conda create -n cromwell python=3.7.6 pip
-conda activate cromwell
-pip install cromwell-tools
-```
+## Create Job Files
 
-Update `secrets.json` with your Cromwell Server address and credentials:
+You need two files for processing a V(D)J sample - one inputs file and one labels file. Use the following example files to help you create your configuration file:
 
-```bash
-$ cat secrets.json
-{
-    "url": "http://ec2-100-26-170-43.compute-1.amazonaws.com",
-    "username": "****",
-    "password": "****"
-}
-```
+- `configs/template.inputs.json`
+- `configs/template.labels.json`
+
+### Reference
+
+Use one of the URLs below for the reference genome:
 
-## Running Workflow
+Type       | `CellRangerGex.reference`
+---------- | -----------------------------------------------------------------------------
+GRCh38     | `https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz`
+mm10       | `https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz`
 
-Submit your job:
+## Submit Your Job
 
 ```bash
-conda activate cromwell
+conda activate scing
 
 ./submit.sh \
-    -k secrets-aws.json \
-    -i configs/sample.inputs.aws.json \
-    -l configs/sample.labels.aws.json \
+    -k ~/keys/cromwell-secrets.json \
+    -i configs/your-sample.inputs.json \
+    -l configs/your-sample.labels.json \
     -o CellRangerGex.options.aws.json
 ```

make-deployable.sh

@@ -2,7 +2,7 @@
 
 wf_name="cellranger-gex"
 version="6.0.2"
-files="submit.sh CellRangerGex.deps.zip CellRangerGex.wdl CellRangerGex.options.aws.json"
+files="submit.sh CellRangerGex.deps.zip CellRangerGex.wdl CellRangerGex.options.aws.json configs/template.*.json"
 dest="$HOME/scing/bin"
 
 usage()
@@ -36,7 +36,7 @@ mkdir -p ${dest}
 # create a temporary directory and copy files
 path_workdir=`mktemp -d`
 mkdir -p ${path_workdir}/${wf_name}-${version}
-cp ${files} ${path_workdir}/${wf_name}-${version}/
+rsync -Rv ${files} ${path_workdir}/${wf_name}-${version}/
 
 # tar-gzip
 cd ${path_workdir}