Update FASTQC version (#230)

* Update FASTQC version and dependencies

Author: bbimber

SequenceAnalysis/build.gradle

@@ -10,14 +10,10 @@ import java.util.regex.Matcher
 
 repositories {
    mavenCentral()
-   // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk
-   maven {
-      url "https://clojars.org/repo"
-   }
-   // Added for org.clojars.chapmanb:sam
-   maven {
-      url "https://maven.scijava.org/content/groups/public"
-   }
+   // Added for jhdf5 from FASTQC / sequence analysis module
+//   maven {
+//      url "https://maven.scijava.org/content/groups/public/"
+//   }
 }
 
 configurations.all {
@@ -96,16 +92,30 @@ dependencies {
             )
     )
 
+    // NOTE: this maven repo has been unreliable
+//    BuildUtils.addExternalDependency(
+//            project,
+//            new ExternalDependency(
+//                    'cisd:jhdf5:19.04.1',
+//                    'JHDF5',
+//                    'JHDF5',
+//                    'https://unlimited.ethz.ch/display/JHDF/',
+//                    ExternalDependency.BSD_LICENSE_NAME,
+//                    ExternalDependency.BSD_LICENSE_URL,
+//                    'JHDF5 is a Java binding for HDF5. Used by FastQC'
+//            )
+//    )
+
     BuildUtils.addExternalDependency(
             project,
             new ExternalDependency(
-                    'org.clojars.chapmanb:sam:1.96',
-                    'picard tools',
-                    'picard tools',
-                    'http://sourceforge.net/projects/picard/',
+                    'net.iharder:base64:2.3.8',
+                    'Base64',
+                    'Base64',
+                    'http://iharder.net/base64/',
                     ExternalDependency.MIT_LICENSE_NAME,
                     ExternalDependency.MIT_LICENSE_URL,
-                    'Library for working with SAM/BAM files.  Used by FastQC'
+                    'Library for Base64 encoding. Used by FastQC'
             )
     )
     implementation "net.sf.opencsv:opencsv:${opencsvVersion}"

SequenceAnalysis/resources/external/basicHistogram.r

@@ -20,5 +20,8 @@
 # fragments for now.
 
 Illumina Universal Adapter					AGATCGGAAGAG
-Illumina Small RNA Adapter					ATGGAATTCTCG
-Nextera Transposase Sequence				CTGTCTCTTATA
+Illumina Small RNA 3' Adapter				TGGAATTCTCGG
+Illumina Small RNA 5' Adapter				GATCGTCGGACT
+Nextera Transposase Sequence				CTGTCTCTTATA
+PolyA										AAAAAAAAAAAA
+PolyG										GGGGGGGGGGGG

SequenceAnalysis/resources/external/basicScatter.r

@@ -43,7 +43,6 @@ Illumina NlaIII expression Sequencing Primer	CCGACAGGTTCAGAGTTCTACAGTCCGACATG
 Illumina Small RNA Adapter 1					GTTCAGAGTTCTACAGTCCGACGATC
 Illumina Small RNA Adapter 2					TGGAATTCTCGGGTGCCAAGG
 Illumina Small RNA RT Primer					CAAGCAGAAGACGGCATACGA
-Illumina Small RNA PCR Primer 1					CAAGCAGAAGACGGCATACGA
 Illumina Small RNA PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
 Illumina Small RNA Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
 
@@ -84,14 +83,11 @@ Illumina NlaIII Gex PCR Primer 1				CAAGCAGAAGACGGCATACGA
 Illumina NlaIII Gex PCR Primer 2				AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
 Illumina NlaIII Gex Sequencing Primer			CCGACAGGTTCAGAGTTCTACAGTCCGACATG
 
-Illumina Small RNA RT Primer					CAAGCAGAAGACGGCATACGA
 Illumina 5p RNA Adapter							GTTCAGAGTTCTACAGTCCGACGATC
 Illumina RNA Adapter1							TGGAATTCTCGGGTGCCAAGG
 
 Illumina Small RNA 3p Adapter 1					ATCTCGTATGCCGTCTTCTGCTTG
 Illumina Small RNA PCR Primer 1					CAAGCAGAAGACGGCATACGA
-Illumina Small RNA PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
-Illumina Small RNA Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
 
 TruSeq Universal Adapter						AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
 TruSeq Adapter, Index 1							GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
@@ -115,7 +111,7 @@ TruSeq Adapter, Index 19						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACTCTCGTATGC
 TruSeq Adapter, Index 20						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTCTCGTATGCCGTCTTCTGCTTG
 TruSeq Adapter, Index 21						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGTCTCGTATGCCGTCTTCTGCTTG
 TruSeq Adapter, Index 22						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG
-TruSeq Adapter, Index 23						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 23						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCACTCTTCTCGTATGCCGTCTTCTGCTTG
 TruSeq Adapter, Index 25						GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG
 TruSeq Adapter, Index 27						GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTCTCGTATGCCGTCTTCTGCTTG
 
@@ -180,3 +176,11 @@ ABI Solid3 EF1 alpha Sense Primer				CATGTGTGTTGAGAGCTTC
 ABI Solid3 EF1 alpha Antisense Primer			GAAAACCAAAGTGGTCCAC
 ABI Solid3 GAPDH Forward Primer					TTAGCACCCCTGGCCAAGG
 ABI Solid3 GAPDH Reverse Primer					CTTACTCCTTGGAGGCCATG
+
+
+
+Clontech Universal Primer Mix Short				CTAATACGACTCACTATAGGGC
+Clontech Universal Primer Mix Long				CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT
+Clontech SMARTer II A Oligonucleotide			AAGCAGTGGTATCAACGCAGAGTAC
+Clontech SMART CDS Primer II A					AAGCAGTGGTATCAACGCAGAGTACT
+

SequenceAnalysis/resources/external/cisd-jhdf5.jar

@@ -2,7 +2,7 @@
 # module at all by setting the value below to 1 for the
 # modules you want to remove.
 duplication 		ignore 		0
-kmer 				ignore 		0
+kmer 				ignore 		1
 n_content 			ignore 		0
 overrepresented 	ignore 		0
 quality_base 		ignore 		0