Changelog
v4.0.2¶
- Increasing picard memory allocation and num of threads for garbage collection
- ChIP-seq updates: estimated fragment length and more (#450)
- Merge pull request #449 from wong-nw/activeDev
- Bug Fix in integrateBatches.R URD call
v4.0.1¶
- removed AVIA
- Increasing resources for fusion inspector
- Switch to python script
- Python implementation of 'reformat_bed.pl'
- Adding memory for fusion inspector rules
- mm10 error
- Run only for 'hg19' or 'hg38'
- Remove ancient tag
- Fixing STAR fusion perl issue
- Explicitly load Perl
- scRNASeq changes Feb 2020 (#438)
- Changing git version: module git/2.15.1 is no longer available
v4.0.0¶
v3.0.6¶
- Setting activeDev branch to master
- Adding updated viral integrated genome hg38_30+HPV16
- Archiving older viral integrated hg38_28+HPV16 references json
- Explicitly loading perl to aviod: 'Perl module GD::Graph::bars not installed, skipping charts' error
- Replacing hg19_KSHV with hg38_30_KSHV
- Adding "References/" as a cache for old reference files
- Updating targets file text, now changes based on reference genome
- Merge pull request #432 from mtandon09/activeDev
- Specify R version (3.5) because default (3.6) does not have 'magick' installed
- Merge pull request #431 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed gzipped VCF issue with germline calling
- Merge pull request #430 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- updated hg38 PON
- Updating rule pca: prevents race condition due to severe filesystem latency
- Updating rule pca: severe filesystem latency can create race condition when copying over files
- Updating pcacall usage to aviod filesystem latency issues
- RNA-seq Initial QC: Contrasts file not longer required
- ChIP-seq GUI: Adding "contrasts" button to the GUI
- Updating Initial QC RNA-seq Interface: only ask for group information
- Update dryrun file-checking for DEG pipelines only
- Updating DEG Reports for mm10_M21
- Updating karyploter's usage to include mm10_M21
- Adding "mm10_M21" to drop down reference genome
- Adding "mm10_M21" Reference Genome: Built using version M21 (Ensembl 96) annotation
- Adding pycache to gitignore
- Merge pull request #429 from kopardev/activeDev
- tidyverse added to genecounts.R along with writetogz function
- trim_se is now temp too
- tmp is actually temp
- tmp is actually temp
- make trim files temp
- not usin g deeptools anymore for bam2bw ... not doing any smoothing for bigwig files
- bringing back bw creation
- Merge remote-tracking branch 'upstream/activeDev' into activeDev
- Updating STAR from 2.5.2b to 2.7.0f for all RNA-seq references genomes
- changing PcaReport.Rmd genecounts.R rsemcounts.R to account for the scenario that we have only 1 group
- Adding compatibility for "ref_vAnnotation" formatted reference genomes
- Removing Strand-specific BigWigs as a target file
- tabs converted to 4 spaces
- bam2bw bc fix
- renaming bam2bw in rnaseq to bam2bw_rnaseq... and increasing its ram to 120g and cpus to 56
- Adding hg38_30 to pipeliner's user interface
- Adding support for hg38_30 to karyoploter.R
- Updating DEG Reports for hg38_30
- Updating PATH to KARYOPLOTER
- Updating the version of STAR from 2.5.2b to 2.7.0f
- Adding hg38_30 references using GENCODE version 30 annotation of the human genome (GRCh38)
- Merge pull request #428 from kopardev/activeDev
- added missing tail -n1 bam2bw rule
- Merge pull request #427 from kopardev/activeDev
- D1.0 type fixed to 1.0 in bam2bw rule
- Merge pull request #426 from jlac/activeDev
- updated STARfusion and FusionInspector, added merged final fusion outputs across 2 callers
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- updated STARfusion, fusioncatcher, and FusionInspector versions
- cluster.json ... partition fixed back to norm only
- Merge pull request #425 from kopardev/activeDev
- Deeptools rule now outputs bigwig files to bams folder
- Deeptools rule all wildcard fix
- Deeptools rule all indentation error fix
- rule all edited to add bam2bw outputs
- Merge pull request #424 from kopardev/activeDev
- rpsd fix
- forward-prob fix for rsem
- file2 defined for se rsem rule
- adding strand specificity to rsem counts command; adding rule to convert bams to forward and reverse bigwigs for easy visualization
- Merge pull request #423 from tovahmarkowitz/activeDev
- fixed bug in gem rule
- DiffBind,uropa,homer,manorm
- homer,uropa,manorm,diffbind,jaccard
- added BCFtools variant QC
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- homer,manorm,uropa,protcoding
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added new fusion rules
- removed target selection from polished germline WES variants; added BCFtools stats QC; substituted Agilent SS v7 target BED file for default targets
- update to mm9/mm10 json files... blacklist bwa index now includes chr_rDNA as well
- merging with main branch nggerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Changing effective genome size and adding differential binding analysis
- Added warning message to "karyoploter.R"
- Adding DEG Type prefix to output karyplot to prevent race conditions
- Adding last reference files for "karoploter.R"
- Adding gene expression karyoploter script
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Marked Qualimap Counts to be moved to DEG
- Updating GUI title
- Updating version to "4.0" for activeDev pipelines
- Updating "activeDev" Pipeliner branch version to 4.0
- Merge pull request #422 from jlac/activeDev
- Adding "karyotxt" reference file to DESeq2, edgeR, limma calls
- Updating LimmaReport Rmarkdown
- Updating EdgerReport Rmarkdown
- Updating DESeq2 Rmarkdown
- Adding karyoploter reference file to organism json files
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- expanded MAF annotation to merged somatic variants
- Updating EBSeq.py Script
- Updating Ebseq rules
- Adding 'hg38_HPV16' to GUI
- Adding resources for hg38_HPV16: hg38_HPV16.json
- Merge pull request #421 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- reduced verbosity of VarDictt to decrease slurm log file size
- Adding hg19_KSHV reference files and updating GUI
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Updating QualiMap commands
- Merge pull request #420 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added multi-caller somatic variant detection to tumor-normal pipelines
- Adding QualiMap bamQC and QualiMap counts
- Updating path to RNA-seq MultiQC config file
- Adding adding qualimap sources to json files
- Adding support for edge-case: group CPM and MINSAMPLE filtering 0 0 (i.e. no filtering)
- completed multi-caller additions to tumor-only somatic pipeline
- Adding rule 'pca' to cluster.json
- fixed bugs in expanded WES tumor only pipeline; changed admixture outputs to all be printed in admixture_out; incorporated vardict somatic calling
- added Vardict tumor only somatic caller, added joint calling with 3 callers for tumor only calling
- improving HOMER/UROPA speeds
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #417 from tovahmarkowitz/activeDev
- adding spearman correlation heatmap to multiQC
- adding to the multiQC report
- removed mtDNA from germline genotyping
- Updating 'rule QCstats' to grab the fragment Length
- Updating to 'filterMetrics' to accept fragLen as an argument
- improving multiqc report, deeptools runtime, and other details
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug in admixture plot generation
- Resolves #416: use the project directory's 'cluster.json' file
- Merge pull request #408 from tovahmarkowitz/activeDev
- begin tracking R scripts for generating sample network and admixture PNGs
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added conversion of sample network to PNG and embedding it in multiQC report
- updates to gui by Vishal
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Resolves #415, added canFam3 and Mmul_8.0.1 to gui
- added summary figure generation and P-value annotation for FREEC CNVs
- Adding Macaca mulatta (Mmul_8.0.1) and Canis_lupus_familiaris (canFam3) reference files
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- adding vardict calling and multi-callier merging
- e for your changes. Lines starting
- rsemcount.R but fix... columns were getting duplicate names
- Updating STAR-p1 arguement: "clip3pAdapterSeq" to "--clip3pAdapterSeq"
- contrasts.tab now accepts 2, 3 or 4 columns, accepts numbers or fraction as column 4, fraction as to be >=0.5 and <1, numbers have to be integers; both numbers and fractions now denote number of samples or fraction of samples PER GROUP where GROUP is one of the groups in the contrast. Filtering of genes in DEG_ALL is changed from 0.5 CPM cutoff of atleast 2 samples out of all the samples to 0.5,0.5 setting ie., 50% of the samples PER GROUP should have atleast 0.5 CPM.
- more memory for ngsqc
- multiqc update and uropa update
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #406 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug in prep_mafs.pl script
- Updating ambiguous Subread genes output filename
- uropa fixes and cluster.json update
- filtersamples.R: changed .. 4th column in contrasts.tab now denotes the number of samples PER GROUP that are required to meet the CPM threshold denoted in column 3 of the same file. If number in column 4 is greater than number of samples in the group, then MINCOUNT is reset to the number of samples in the group.
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Resolves #405, 'preseq lc_extrap' approximation
- uropa temporary workaround
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #404 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- improved somatic variant fitlering and maftools summaries
- merging branches
- adding uropa and other changes to chip-seq pipeline
- PhantomPeakQualTool: Bigwig Generation from Estimated Fragment Length, resolves #403
- Updated Heatmap Height and PCA report generation (when > 100 samples)
- fixing issues caused by lack of input or PE sequencing data
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #401 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug in WES BED file generation where empty files are written when an incorrect path to target bed is given
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #400 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- moved sort out of STAR and into samtools rule to deal with memory bug
- PcaReport Rmarkdown Fix: Before Normalization/DESeq2 #399
- reworked ChIPseq.snakefile with improvements
- Merge pull request #394 from tovahmarkowitz/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #398 from jlac/activeDev
- added memory limit to STAR 2-pass in rnaseqvarcalling
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug in 2nd pass of freec
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #397 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug tracking FREEC 2nd pass output
- gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #396 from jlac/activeDev
- completed new CNV workflow for WES and WGS
- implementing 2-pass FREEC and Sequenza to WES and WGS pipelines
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- completed sequenza rule for WES and WGS, and completed second-pass rules for 2-pass freec
- added multipass freec CNV analysis to use ploidy and purity prior from sequenza
- tracking new files and scripts to run FREEC and sequenza
- added FREEC to tumor only pipeline, and sequenza and freec to tumor-normal pipeline
- updated Canvas germline to most recent version, and fixed bugs
- updated Canvas and fixed bugs in Canvas somatic CNV calling
- fixed error with ngsqc_plot rule
- adding ngsqc plot feature
- adding macs2 dedup functionality
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added full germline calling to wgs tumor-only pipeline
- added full germline genotyping to all somatic pipelines
- Merge pull request #389 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- updated GATK version to 3.8 in combine somatic GVCFs, and switched to filtering all MAF files with perl script rather than in maftools
- Merge pull request #388 from tovahmarkowitz/activeDev
- fixed fingerprint plot and multiQC
- Fix: WES Slurm Master Job Failure
- WGS/WES Reference Genome Selection Warning Message #377
- Merge pull request #376 from tovahmarkowitz/activeDev
- Update cluster.json
- Initial ChIP-seq QC DAG SVG Generation, Updated Peaking Calling Rules, Generated MEMEchip Reference Files #375
- fixed ppqt
- bak files removed; cutadapt updated to 1.18 on rnaseq
- fixing .gitignore
- Fixed ChIP-seq Python Package ImportError #374
- Fixed ChIP-seq Python Package ImportError #374
- Merge pull request #1 from vnkoparde/activeDev
- changing cutadapt in initial chipseq qc snakefile from 1.16 to 1.18 and adding a ppqt_pe rule
- actual purge and adding .DS_Store to the list
- adding .gitignore to ignore .* *.bak and *~ files
- standard-bin.json changed to change version of cutadapt from 1.16 to 1.18
- Rolling back InitialChIP Seq snakefile to commit ac47e92a20af8de3fe1ddd9344c613dc38f9cf63
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- In PE mode readlength based filters to be applied to any (not both) of the the reads
- Merge pull request #373 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added automated filtering to prep_mafs.pl script
- Python Package Import Incomaptiblity Fix: pysam
- chipseq:cutadapt to v 1.18, remove files ending in tilda, added .gitignore, added separate ppqt rules for se and pe
- Labels Testing: unbound variable fix
- updated genome fasta for rnaseqvarcalling for mm10
- Labels file edge case: peak call pop-up box fix
- Copy peakcall.tab if labels.txt in rawdata directory
- merge with main pipeline gerge th otherbranch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- ltered somatic variant filtering to be based on alt and ref counts in tumor sample, instead of allele frequency
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Explicitly Loading Snakemake Module #371
- Explicitly Loading Snakemake Module #371
- fixed somatic directory creation bug due to snakemake version change
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixed bug in loading VEP and vcf2maf for MAF generation rules
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev combining pipelines :gibincomninge enter a commit message to explain why this merge is necessary,
- separating fingerprint plots; merging inputnorm heatmaps
- Update README.md
- Update README.md
- readding geneinfo to chipseq
- fixing merge issue
- merging with CCBR/activeDev gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Dynamically Resolve CCR BUY-IN NODES ISSUE #358
- Dynamically Resolve BUY-IN NODE Issue #358
- RSEM CPM filtering Issue #357
- json merge issue
- merging json files
- Removed an include statement
- Updated GEM GEMONECHRS
- Merge pull request #356 from jlac/activeDev
- updated splitNcigar GATK version to 3.8
- Re-validated cluster.json file
- fix error with read extension
- gerge with Justin's changes branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Changing Partition from 'ccr,norm' to 'norm'
- Merge pull request #355 from jlac/activeDev
- reduced wall times for rules that do not need max wall time
- changed default partition to norm
- renaming bws
- changing bw naming
- Update Deeptools PE Target Rule
- Resolving Deeptools Filenames
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added indexing rule to all WGS and WES pipelines
- playing with dependencies
- merge with other pipelines branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #351 from jlac/activeDev
- repaired wgs_tumor_only bug in maftools
- merging ChIP-seq with other pipelines gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- CPM Filtering Fix
- Use Updated Sampletable for PCA
- Export RSTUDIO_PANDOC
- merging with Paul's function gerge branch 'activeDev' of https://github.com/tovahmarkowitz/Pipeliner into activeDev
- merging with Justin's changes gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Inputnorm rule integration
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- increased master job wall time to 10 days
- Merge pull request #350 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- made theta2 outputs dynamic to allow pipeline to complete under conditions where the theta2 rule fails
- read extension for bigwigs and dynamic deeptools rules
- merge with Justin's changes branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #349 from jlac/activeDev
- added chr prefix to hg38 chromosome names in haplotype caller rules split by chromosome
- merging with contrasts.tab changes Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added filtering for MAF files, and added additional summary plot and analysis of MAF files
- Safe-guards to ensure referential integrity during differential expression analysis
- Updating rule pca
- adding heatmaps and profile plots
- merging changes with ChIP-seq and RNA-seq pipelinesMerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Pop-up box warning if 'groups.tab' or 'contrast.tab' are not in RNA-seq working directory before dry-running
- pcacall.R revert
- removed some pointers
- changed conditions for trim_pe and trim_se
- combining structural annotation information and chip-seq file pointers Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #348 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- split rnaseqvarcalling by chromosome
- Adjusting different rules in IniitialChIPseq.snakefile merge branch 'activeDev' of https://github.com/tovahmarkowitz/Pipeliner into activeDev
- changes made to both exome-seq and chip-seq portions of hg19.json Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Merge pull request #347 from jlac/activeDev
- fixed bug in location of fusion STAR libraries
- add peakcall.tab parsing and rule inputnorm (not implemented)
- new heatmap rule
- adding GENEINFO to ChIP-seq
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- fixing thread usage
- Merge pull request #345 from jlac/activeDev
- 'peakcall.tab' is copied over if it's in the data directory
- bug fixes with deeptools_QC
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- increased the number of jobs submitted at a time to 500
- bug fixes
- adding fingerprint plot
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev changes to RNA-seq merged with changes to ChIP-seq:
- Merge branch 'kopardev-activeDev' into activeDev 344 pr updates
- 344 pr updates
- split haplotype caller by chromosome for all germline pipelines
- removed Delly from all pipelines
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- added knwn ploidy config file to mm10.json for running Canvas
- Rename symlinked bams to .recal.bam
- Genome-seq/Exome-seq symlink update to work with labels.txt file
- fixed bug
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- GUI Changes: peakcall.tab now required for InitialChIPseqQC
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Symlink BAM and VCF files for Exome-seq/Genome-seq
- fixed rule connections
- fixed indentation error
- organized rules
- cleaning script for clarity
- consolidating rules
- updated MallDoneerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- repaired starfusion bug and hg38 exome somatic only bug
- cleaned up code
- Merge pull request #343 from jlac/activeDev
- updated versions for STARfusion and Canvas, and updated annotation resources for STARfusion to the most recent. Also, added multithreading to STARfusion
- fixed bug in all rule for wgs somatic tumor-only
- stepped back to v0.9.1 for cnvkit due to python bug
- RNA-seq DEG changes
- Syntax Error: removing extra parentheses
- Undo reading in files in binary mode
- Low Abundance Gene Thresholds option removed from the DEG gui frame ... this data is now entered in the contrasts.tab
- rRNA list fixed for mm9
- Merge pull request #342 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- updated snpeff genome version for mouse
- Merge pull request #341 from jlac/activeDev
- changed hg38 filter ExAC VCF
- adding warnings for selecting the wrong genome ... for eg. GRCh38 will only work with scRNASeq pipeline ... pop up warning if it is selected for other pipeline
- adding decoy genomes for RNASeq/ChIPSeq pipelines ... updating annotations for other genomes
- new mouse RNASeq and ChIPSeq indexes included in json files
- Fixed indention inconsistency
- QCTable NReads Fix
- add sample info to initialrnaseqqc gui; added mincount column to groups.tab
- Merge pull request #339 from jlac/activeDev
- updated hatplotype caller steps to GATK 3.8-0, fixed jdk inflater bug, and added index BAMs step to Dragen entry point
- Adding peakcaller GEM
- ChIP-seq QC Table
- Merge pull request #338 from jlac/activeDev
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev updating
- updated Canvas version from 1.31 to 1.35
- ChIP-seq Multiqc: Samtools Flagstat and Fastq Screen
- Delete PipelinerVer1.0_documentation.pdf
- Delete PipelinerVer1.0_documentation.docx
- Delete PipelinerVer1.0_documentation.pdf
- Delete PipelinerVer1.0_documentation.docx
- Filename bug fix
- Snakemake DAG generation fix
- filtersample scripts
- DEG_ALL folder ... extra column for contrasts.tab to have different cutoffs
- increased memory for qualimap rules
- Label Name Fix
- Merge pull request #332 from CCBR/revert-331-activeDev
- Revert "test commit"
- Merge pull request #331 from pajailwala/activeDev
- test commit
- Venn Diagram Additions
- deleting test
- Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into activeDev
- Update README.md
- avia curl request fix
- test2
- testing
- Venn Diagram showing overlap of DE genes
- Reformatted Limma, DESeq2, EdgeR Output: RNASeq
v3.0.5¶
- ChIP-seq bug fix and gui additions
- Merge pull request #322 from nikhilbg/centosOS7
- minor bugfix for annotationdbi usage in scrnaseq
- cell cycle regression option in scrnaseq
- Nihkil changes for Single Cell
v3.0.4¶
v3.0.3¶
v3.0.2¶
v3.0.1¶
v3.0.0¶
- multiqc is now not running in DEG part
- Merge pull request #316 from jlac/master
- updated versions for cnvkit and manta
- Merge pull request #315 from abdallahamr/master
- This is for the cpm filtering as it was not doing cpm twice, I only commented out one line per file
- Merge pull request #314 from jlac/master
- removed realign and recal from WES somatic and germline calling stages of WES pipelines
- Merge pull request #313 from CCBR/v3.0branch
- data/work folder is copy paste on gui... workflow error fix
- Merge pull request #312 from jlac/master
- Merge remote branch 'upstream/master'
- updates version of multiqc to v1.3
- Merge pull request #311 from jlac/master
- fixed bugs in fusion expression cleanup
- Merge pull request #310 from jlac/master
- Merge remote branch 'upstream/master'
- changed path to Oncofuse jar file
- Merge pull request #309 from jlac/master
- removed subread components from gene expression rules for fusion pipeline
- Merge remote branch 'upstream/master'
- changed filtering criteria for MAF filtering
- fixed bug in processing tumor-only maftools rule
- Merge pull request #308 from jlac/master
- Merge remote branch 'upstream/master'
- added filtering to somatic mutation calls; fixed jsons to repair missing resources in fusion and rnaseqvar pipelines
- Merge pull request #307 from jlac/master
- fixed Canvas version module
- Merge pull request #306 from jlac/master
- repaired missing reference resources for fusion and ranseqvar pipelines
- fixed bug in counting sample for mutsigCV
- Merge pull request #305 from jlac/master
- Merge remote branch 'upstream/master'
- added population allele frequencies to MAF filtering, and set mutsig a threshold of 10 samples or tumor/normal pairs for mutsig to run
- Merge pull request #304 from jlac/master
- Merge remote branch 'upstream/master'
- fixed X11 graphics bug in qualimap
- Merge remote branch 'upstream/master'
- removed extraneous file
Last update: 2022-11-04