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bbimber wants to merge 6 commits into from
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Merge discvr-20.7 to develop #54

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f65aef1
Add support for cellranger vdj --inner-enrichment-primers
bbimber Nov 4, 2020
cbf62fe
Add support for cellranger vdj --disable-ui
bbimber Nov 4, 2020
633d7f4
Larger input and validation for cellranger primer input
bbimber Nov 4, 2020
039f82a
cellranger param is a switch
bbimber Nov 4, 2020
e0cb5a7
Fix param name
bbimber Nov 4, 2020
17dca69
Merge discvr-20.7 to develop
bbimber Nov 6, 2020
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2 changes: 1 addition & 1 deletion tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java
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Expand Up@@ -248,7 +248,7 @@ public static File processBarcodeFile(SequenceOutputHandler.JobContext ctx, File
//prepare whitelist of cell indexes
File cellBarcodeWhitelist = utils.getValidCellIndexFile();
Set<String> uniqueBarcodes = new HashSet<>();
ctx.getLogger().debug("writing cell barcodes");
ctx.getLogger().debug("writing cell barcodes, using file: " + perCellTsv.getPath());
try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER);CSVReader reader = new CSVReader(IOUtil.openFileForBufferedUtf8Reading(perCellTsv), '\t'))
{
int rowIdx = 0;
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2 changes: 1 addition & 1 deletion tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
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Expand Up@@ -376,7 +376,7 @@ public File runRemoteVdjCellHashingTasks(PipelineStepOutput output, String outpu
File cellBarcodeWhitelist = getValidCellIndexFile();
Set<String> uniqueBarcodes = new HashSet<>();
Set<String> uniqueBarcodesIncludingNoCDR3 = new HashSet<>();
_log.debug("writing cell barcodes");
_log.debug("writing cell barcodes, using file: " + perCellTsv.getPath());
try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER); CSVReader reader = new CSVReader(Readers.getReader(perCellTsv), ','))
{
int rowIdx = 0;
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34 changes: 34 additions & 0 deletions tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java
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Expand Up@@ -68,6 +68,7 @@ public CellRangerVDJWrapper(@Nullable Logger logger)

public static final String TARGET_ASSAY = "targetAssay";
public static final String DELETE_EXISTING_ASSAY_DATA = "deleteExistingAssayData";
public static final String INNER_ENRICHMENT_PRIMERS = "innerEnrichmentPrimers";

public static class VDJProvider extends AbstractAlignmentStepProvider<AlignmentStep>
{
Expand All@@ -82,6 +83,13 @@ public VDJProvider()
ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{
put("minValue", 0);
}}, null),
ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--disable-ui"), "disable-ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{
put("checked", true);
}}, true),
ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textarea", new JSONObject(){{
put("height", 100);
put("width", 400);
}}, null),
ToolParameterDescriptor.create(TARGET_ASSAY, "Target Assay", "Results will be loaded into this assay. If no assay is selected, a table will be created with nothing in the DB.", "tcr-assayselectorfield", new JSONObject(){{
put("autoSelectAssay", false);
}}, null),
Expand DownExpand Up@@ -296,6 +304,32 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, File inputFast
File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
args.add("--reference=" + indexDir.getPath());

String primers = StringUtils.trimToNull(getProvider().getParameterByName(INNER_ENRICHMENT_PRIMERS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
if (primers != null)
{
primers = primers.replaceAll("\\s+", ",");
primers = primers.replaceAll(",+", ",");

File primerFile = new File(outputDirectory, "primers.txt");
try (PrintWriter writer = PrintWriters.getPrintWriter(primerFile))
{
Arrays.stream(primers.split(",")).forEach(x -> {
x = StringUtils.trimToNull(x);
if (x != null)
{
writer.println(x);
}
});
}
catch (IOException e)
{
throw new PipelineJobException(e);
}

output.addIntermediateFile(primerFile);
args.add("--inner-enrichment-primers=" + primerFile.getPath());
}

args.addAll(getClientCommandArgs("="));

Integer maxThreads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
Expand Down