Major refactor to split out single-cell code into new module

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -17,7 +17,6 @@
 
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.laboratory.NavItem;
@@ -88,10 +87,6 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public String getVCFLineCount(File vcf, Logger log, boolean passOnly) throws PipelineJobException;
 
-    abstract public File writeAllCellHashingBarcodes(File webserverDir, User u, Container c) throws PipelineJobException;
-
-    abstract public File writeAllCiteSeqBarcodes(File webserverDir, User u, Container c) throws PipelineJobException;
-
     abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers) throws IOException;
 
     abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers, Set<GenomeTrigger> extraTriggers) throws IOException;
@@ -103,4 +98,6 @@ static public void setInstance(SequenceAnalysisService instance)
     abstract public void sortGxf(Logger log, File input, @Nullable File output) throws PipelineJobException;
 
     abstract public void ensureFeatureFileIndex(File input, Logger log) throws PipelineJobException;
+
+    abstract public void mergeFastqFiles(File output, List<File> inputs, Logger log) throws PipelineJobException;
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -18,12 +18,10 @@
 
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
-import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.sequenceanalysis.run.CommandWrapper;
 
 import java.io.File;
@@ -126,6 +124,4 @@ static public void setInstance(SequencePipelineService instance)
     abstract public void updateOutputFile(SequenceOutputFile o, PipelineJob job, Integer runId, Integer analysisId);
 
     abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
-
-    abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls, boolean createOutputFiles, boolean useSeurat, boolean useMultiSeq) throws PipelineJobException;
 }

SequenceAnalysis/resources/credits/jars.txt

@@ -6,6 +6,6 @@ biojava3-core-3.0.7.jar|biojava3-core|3.0.7|{link:biojava|http://biojava.org/wik
 biojava3-genome-3.0.7.jar|biojava3-genome|3.0.7|{link:biojava|http://biojava.org/wiki/Main_Page}|{link:GNU Lesser GPL V2.1|http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}|bbimber|Java framework for processing biological data
 commons-math3-3.6.1.jar|commons-math|3-3.6.1|{link:commons-math|http://commons.apache.org/proper/commons-math/}|{link:Apache License, Version 2.0|http://www.apache.org/licenses/LICENSE-2.0.txt}|bbimber|Self-contained mathematics and statistics components
 commons-net-3.5.jar|Commons Net|3.3|{link:Apache|http://jakarta.apache.org/commons/net/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|bbimber|FTPClient used to retrieve resources from other servers (e.g., GO annotations)
-htsjdk-2.21.3.jar|htsjdk|2.21.3|{link:htsjdk|http://samtools.github.io/htsjdk/}|{link:MIT License|http://opensource.org/licenses/MIT}|bbimber|Description	A Java API for high-throughput sequencing data (HTS) formats
+htsjdk-2.21.3.jar|htsjdk|2.21.3|{link:htsjdk|http://samtools.github.io/htsjdk/}|{link:MIT License|http://opensource.org/licenses/MIT}|bbimber|A Java API for high-throughput sequencing data (HTS) formats
 picard-2.22.4.jar|Picard Tools Lib|2.22.4|{link:PicardTools|https://github.com/broadinstitute/picard}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|bbimber|Manipulating Sequence Data
 {table}