Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update FASTQC version #230

Merged
merged 4 commits into from
Aug 29, 2023
Merged

Update FASTQC version #230

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
92d9493
Update FASTQC version and dependencies
bbimber Aug 29, 2023
a3b2162
Remove unused files
bbimber Aug 29, 2023
06ba133
Bugfixes
bbimber Aug 29, 2023
1f0218f
Switch to StringBuilder within loop
bbimber Aug 29, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 23 additions & 13 deletions SequenceAnalysis/build.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down Expand Up @@ -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}"
Expand Down
62 changes: 0 additions & 62 deletions SequenceAnalysis/resources/external/basicHistogram.r
View file
Open in desktop

This file was deleted.

55 changes: 0 additions & 55 deletions SequenceAnalysis/resources/external/basicScatter.r
View file
Open in desktop

This file was deleted.

Binary file added SequenceAnalysis/resources/external/cisd-jhdf5.jar
View file
Open in desktop
Binary file not shown.
64 changes: 0 additions & 64 deletions SequenceAnalysis/resources/external/coverageGraph.r
View file
Open in desktop

This file was deleted.

7 changes: 5 additions & 2 deletions SequenceAnalysis/resources/external/fastqc/Configuration/adapter_list.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
14 changes: 9 additions & 5 deletions SequenceAnalysis/resources/external/fastqc/Configuration/contaminant_list.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand All @@ -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

Expand Down Expand Up @@ -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

2 changes: 1 addition & 1 deletion SequenceAnalysis/resources/external/fastqc/Configuration/limits.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Loading