Add basic QC notebook

Author: hisplan

CiteSeq.wdl

@@ -1,6 +1,7 @@
 version 1.0
 
 import "modules/Preprocess.wdl" as Preprocess
+import "modules/BasicQC.wdl" as BasicQC
 
 workflow CiteSeq {
 
@@ -76,6 +77,16 @@ workflow CiteSeq {
             resourceSpec = resourceSpec,
             dockerRegistry = dockerRegistry
     }
+    
+    call BasicQC.BasicQC {
+        input:
+            sampleName = sampleName,
+            h5ad = Preprocess.adata,
+            readsCount = Preprocess.readCountMatrix,
+            runReport = Preprocess.countReport,
+            templateNotebook = "inspect-citeseq-v3.ipynb",
+            dockerRegistry = dockerRegistry
+    }
 
     output {
         File fastQCR1Html = Preprocess.fastQCR1Html
@@ -86,5 +97,9 @@ workflow CiteSeq {
         Array[File] readCountMatrix = Preprocess.readCountMatrix
 
         File adata = Preprocess.adata
+
+        File notebookQC = BasicQC.notebook
+        File htmlQC = BasicQC.htmlReport
+        File adataQC = BasicQC.adata        
     }
 }

Hashtag.wdl

@@ -5,6 +5,7 @@ import "modules/HtoDemuxSeurat.wdl" as HtoDemuxSeurat
 import "modules/HtoDemuxKMeans.wdl" as HtoDemuxKMeans
 import "modules/Combine.wdl" as Combine
 import "modules/AnnData.wdl" as AnnData
+import "modules/BasicQC.wdl" as BasicQC
 
 workflow Hashtag {
 
@@ -140,6 +141,16 @@ workflow Hashtag {
             dockerRegistry = dockerRegistry
     }
 
+    call BasicQC.BasicQC {
+        input:
+            sampleName = sampleName,
+            h5ad = UpdateAnnData.outAdata,
+            readsCount = Preprocess.readCountMatrix,
+            runReport = Preprocess.countReport,
+            templateNotebook = "inspect-hashtag-v3.ipynb",
+            dockerRegistry = dockerRegistry
+    }
+
     output {
         File fastQCR1Html = Preprocess.fastQCR1Html
         File fastQCR2Html = Preprocess.fastQCR2Html
@@ -166,5 +177,9 @@ workflow Hashtag {
 
         File adataRaw = Preprocess.adata
         File adataFinal = UpdateAnnData.outAdata
+
+        File notebookQC = BasicQC.notebook
+        File htmlQC = BasicQC.htmlReport
+        File adataQC = BasicQC.adata
     }
 }

dockers/basic-qc/Dockerfile

@@ -0,0 +1,14 @@
+FROM quay.io/hisplan/scri-notebook:0.0.3
+
+LABEL maintainer="Jaeyoung Chun ([email protected])"
+
+RUN apt-get install -y zip
+
+RUN pip install seaborn==0.11.1 matplotlib humanfriendly
+        
+# hack: nbcovert 6+ doesn't work properly to run `nbconvert --to html_toc`
+RUN pip install nbconvert==5.6.1 jupyter_contrib_nbextensions==0.5.1
+RUN jupyter contrib nbextension install --user \
+    && jupyter nbextension enable toc2
+
+COPY ./notebooks/inspect-*.ipynb /opt/

dockers/basic-qc/README.md

@@ -0,0 +1,13 @@
+# sharp-basic-qc
+
+Enter into the Jupyter Notebook container:
+
+```bash
+./run-notebook.sh
+```
+
+When you get a prompt back, launch Jupyter Notebook:
+
+```bash
+jupyter notebook --allow-root
+```

dockers/basic-qc/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -e
+
+source config.sh
+
+docker build -t ${image_name}:${version} .

dockers/basic-qc/config.sh

@@ -0,0 +1,5 @@
+version="0.2.0"
+
+# docker related
+registry="quay.io/hisplan"
+image_name="sharp-basic-qc"