Fix docker syntax

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java

@@ -52,7 +52,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
             writer.println("sudo $DOCKER run --rm=true \\");
             writer.println("\t-v \"${WD}:/work\" \\");
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
-            _ctx.getDockerVolumes().forEach(writer::println);
+            _ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             if (_tmpDir != null)
             {
                 writer.println("\t-v \"" + _tmpDir.getPath() + ":/tmp\" \\");

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java

@@ -291,7 +291,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 writer.println("sudo $DOCKER run --rm=true \\");
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
-                ctx.getDockerVolumes().forEach(writer::println);
+                ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
                 writer.println("\t -w /work \\");
                 if (!StringUtils.isEmpty(System.getenv("TMPDIR")))
                 {

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java

@@ -270,7 +270,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, boolean retai
                 writer.println("sudo $DOCKER run --rm=true \\");
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
-                ctx.getDockerVolumes().forEach(writer::println);
+                ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
                 if (!StringUtils.isEmpty(System.getenv("TMPDIR")))
                 {
                     writer.println("\t-v \"${TMPDIR}:/tmp\" \\");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java

@@ -184,7 +184,7 @@ public static File runNextClade(File consensusFasta, Logger log, PipelineOutputT
             }
 
             writer.println("\t-v \"${WD}:/work\" \\");
-            ctx.getDockerVolumes().forEach(writer::println);
+            ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");
             writer.println("\t-w /work \\");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PangolinHandler.java

@@ -308,7 +308,7 @@ private static File runUsingDocker(File outputDir, Logger log, File consensusFas
 
             String extraArgString = extraArgs == null ? "" : " " + StringUtils.join(extraArgs, " ");
             writer.println("\t-v \"${WD}:/work\" \\");
-            ctx.getDockerVolumes().forEach(writer::println);
+            ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");
             writer.println("\t-w /work \\");

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -350,7 +350,7 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             File tmpDir = new File(SequencePipelineService.get().getJavaTempDir());
             writer.println("\t-v \"${WD}:/work\" \\");
             writer.println("\t-v \"" + tmpDir.getPath() + ":/tmp\" \\");
-            ctx.getDockerVolumes().forEach(writer::println);
+            ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1326,7 +1326,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
 
             writer.println("\t-e CELLHASHR_DEBUG=1 \\");
             writer.println("\t-v \"${WD}:/work\" \\");
-            ctx.getDockerVolumes().forEach(writer::println);
+            ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -592,7 +592,7 @@ private boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutput outpu
                 writer.println("\t--memory='" + maxRam + "g' \\");
             }
 
-            getPipelineCtx().getDockerVolumes().forEach(writer::println);
+            getPipelineCtx().getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${WD}:/work\" \\");
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
             writer.println("\t-u $UID \\");