Update README.md

README.md

@@ -1,66 +1,27 @@
 # velopipe
 
-Pipeline for RNA Velocity using Velocyto & scVelo
+RNA Velocity for SEQC
 
 ## Setup
 
-```bash
-aws s3 cp s3://dp-lab-home/software/install-Velopipe-0.0.7.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.
 
-## Preparing Job File
+## Create Job Files
 
-You need to provide two JSON files that describes your job:
+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:
 
-### ${sample-name}.inputs.json
+- `config/template.inputs.json`
+- `config/template.labels.json`
 
-```json
-{
-    "Velopipe.countsMatrix": "s3://dp-lab-data/collaborators/pi/project/sample/..._dense.csv",
-    "Velopipe.bam": "s3://dp-lab-data/collaborators/pi/project/sample/..._Aligned.out.sorted.bam",
-    "Velopipe.bai": "s3://dp-lab-data/collaborators/pi/project/sample/..._Aligned.out.sorted.bam.bai",
-    "Velopipe.gtf": "s3://seqc-public/genomes/mm38_long_polya/annotations.gtf",
-    "Velopipe.barcodeWhitelist": "s3://seqc-public/barcodes/ten_x_v3/flat/3M-february-2018.txt",
-    "Velopipe.alreadySortedBam": true
-}
-```
+For more information, please refer to [this page](docs/velopipe2-how-to-create-job-file.md):
 
-- `Velopipe.countMatrix`: a file from which filtered barcodes will be extracted
-  - dense matrix file (e.g. `*_dense.csv`)
-  - barcodes file to construct the sparse matrix (e.g. `*_sparse_counts_barcodes.csv`)
-- `Velopipe.bam`: BAM file generated by SEQC
-- `Velopipe.bai`: BAM index file
-- `Velopipe.gtf`: GTF file
-  - Human: `s3://seqc-public/genomes/hg38_long_polya/annotations.gtf`
-  - Mouse: `s3://seqc-public/genomes/mm38_long_polya/annotations.gtf`
-- `Velopipe.barcodeWhitelist`: a barcode whitelist
-  - 10x v2: `s3://seqc-public/barcodes/ten_x_v2/flat/737K-august-2016.txt`
-  - 10x v3: `s3://seqc-public/barcodes/ten_x_v3/flat/3M-february-2018.txt`
-- `Velopipe.alreadySortedBam`: `true` if the BAM file is already position sorted
-
-### ${sample-name}.labels.json
-
-```json
-{
-    "pipelineType": "Velopipe",
-    "project": "Project 193",
-    "sample": "1469_TGFb_LCC-TRL_1_P193",
-    "owner": "chunj",
-    "destination": "s3://dp-lab-data/Siting/TGFb_LCC_TRL1",
-    "transfer": "-",
-    "comment": "RNA Velocity"
-}
-```
-
-- `project`: project ID retrieved from SCRI database
-- `sample`: sample name
-- `destination`: AWS S3 location where the final output files (e.g. loom) should be saved
-
-## Submitting a Job
+## Submit Your Job
 
 ```bash
+conda activate scing
+
 ./submit.sh \
-    -k ~/secrets-aws.json \
+    -k ~/keys/cromwell-secrets.json \
     -i config/your-sample.inputs.json \
     -l config/your-sample.labels.json \
     -o Velopipe.options.aws.json

make-deployable.sh

@@ -2,7 +2,7 @@
 
 wf_name="velopipe"
 version="0.0.7"
-files="submit.sh Velopipe2.wdl Velopipe.deps.zip Velopipe.options.aws.json"
+files="submit.sh Velopipe2.wdl Velopipe.deps.zip Velopipe.options.aws.json config/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}