Merge pull request #39 from jhuapl-bio/prerelease

v0.5.1 release

.github/workflows/build_push_docker-prerelease.yml

@@ -0,0 +1,24 @@
+name: Build and push Docker image for pre-release
+
+on:
+  push:
+    branches: staging
+
+jobs:
+  push_to_registry:
+    name: Build and push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Push to Docker Hub
+        uses: docker/build-push-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          repository: ${{ secrets.DOCKERHUB_REPOSITORY }}
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: staging

.github/workflows/build_push_docker-dev.yml → .github/workflows/build_push_docker-staging.yml

@@ -1,4 +1,4 @@
-name: Build and push Docker image upon release
+name: Build and push Docker image for staging
 
 on:
   push:
@@ -21,4 +21,4 @@ jobs:
           repository: ${{ secrets.DOCKERHUB_REPOSITORY }}
           tag_with_ref: true
           tag_with_sha: true
-          tags: dev
+          tags: staging

README.md

@@ -1,3 +1,33 @@
 # Basestack consensus
 
 This pipeline is an implementation of the ARTIC network pipeline that is deployed in a Docker container that can be easily installed using the Basestack platform (https://github.com/jhuapl-bio/Basestack).
+
+## Normal usage
+
+Install Basestack as described here: https://github.com/jhuapl-bio/Basestack and install the 'Consensus' module.
+
+## Development usage
+
+The pipeline can be directly run, for development or other command line use, with the following commands:
+
+1. Download the latest version of the pipeline with:
+
+```sh
+docker pull jhuaplbio/basestack_consensus:latest
+```
+
+2. Connect a MinION sequencing run folder to a container of that image:
+
+```sh
+docker container run \
+  --rm \
+  -it \
+  -v /path/to/local/MinION/data:/opt/basestack_consensus/sequencing_runs/example-run \
+  jhuaplbio/basestack_consensus:latest \
+  bash
+```
+
+3. Within the container, run the pipeline on the MinION run folder:
+```sh
+artic-module1-barcode-demux.sh -i /opt/basestack_consensus/sequencing_runs/example-run
+```

pipeline_scripts/report-template.Rmd

@@ -321,9 +321,12 @@ for(i in sample_barcodes) {
 rownames(depth_plot_mean) <- sample_barcodes
 
 # identify low coverage regions
+threshold <- NULL
 if(!is.null(postfilt_all)) {
-  threshold <- as.numeric(postfilt_all$ont_depth_thresh[1])
-} else {
+  numeric_thresholds <- !is.na(as.numeric(postfilt_all$ont_depth_thresh))
+  threshold <- max(as.numeric(postfilt_all$ont_depth_thresh[numeric_thresholds]))
+}
+if(!is.integer(threshold)) {
   threshold <- 20
 }
 #below_threshold <- function(v) { return(v<=threshold) }

pipeline_scripts/report_summary_table.sh

@@ -308,7 +308,26 @@ else
 	echo_log "Demux count already present - will not overwrite it"
 fi
 
-ont_depth_thresh=$(head -n2 "$postfilt_all" | awk -F $'\t' '{if(NR==1){for(i=1; i<=NF; i++){if($i=="ont_depth_thresh"){col=i;}}}else{print $col}}')
+# identify max ONT depth threshold from postfilt_all (default to 20 if non-numeric)
+ont_depth_thresh=$(awk -F $'\t' '{
+	if(NR==1) {
+		for(i=1; i<=NF; i++) {
+			if($i=="ont_depth_thresh") {
+				col=i;
+			}
+		}
+	} else {
+		if($col > thresh) {
+			thresh = $col
+		}
+	}
+} END {
+	if(thresh+1-1 == thresh) {
+		print(thresh);
+	} else {
+		print(20);
+	}
+}' "$postfilt_all")
 echo_log "Depth threshold: $ont_depth_thresh"
 
 echo_log "Reading manifest"