Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / molgenis/molgenis-pipelines issues and pull requests

#640 - Create LICENSE

Pull Request - State: open - Opened by dennishendriksen about 5 years ago

#639 - small updates pipelines

Pull Request - State: open - Opened by npklein almost 6 years ago - 1 comment

#638 - updating pipeline error handling, bug fix, removal semi-hardcoded path

Pull Request - State: closed - Opened by npklein almost 6 years ago

#637 - Version updates, small improvements

Pull Request - State: closed - Opened by npklein almost 6 years ago

#636 - Remove fastq files after CRAMing

Pull Request - State: closed - Opened by npklein about 6 years ago

#635 - Add removal of FastQ files after cramming

Pull Request - State: closed - Opened by npklein about 6 years ago

#634 - Update QC and quantification pipeline

Pull Request - State: closed - Opened by npklein over 6 years ago

#633 - fix broken link

Pull Request - State: closed - Opened by npklein over 6 years ago

#632 - Update mc-start.md

Pull Request - State: closed - Opened by BenjaminsM about 7 years ago

#630 - New 5GPM phasing pipeline

Pull Request - State: closed - Opened by freerkvandijk about 7 years ago - 4 comments

#629 - updated ngs-utils version

Pull Request - State: closed - Opened by freerkvandijk over 7 years ago

#627 - correct workflow

Pull Request - State: closed - Opened by npklein over 7 years ago

#626 - Add chunking protocols for phasing

Pull Request - State: closed - Opened by npklein over 7 years ago

#625 - Filter beagle/PLVCF

Pull Request - State: closed - Opened by npklein over 7 years ago

#624 - removed if/else conditionals from protocols

Pull Request - State: closed - Opened by freerkvandijk over 7 years ago

#623 - Removed if/else conditionals from protocols publicRNAseq

Pull Request - State: closed - Opened by freerkvandijk over 7 years ago - 1 comment

#622 - GenotypeHarmonizer use EBROOT

Pull Request - State: closed - Opened by npklein over 7 years ago

#621 - fix some small bugs, remove some random tabs

Pull Request - State: closed - Opened by npklein over 7 years ago

#620 - Add Convading documentation

Pull Request - State: closed - Opened by mark-de-haan over 7 years ago

#619 - Added GitBook documentation for pipelines repository

Pull Request - State: closed - Opened by mark-de-haan over 7 years ago

#618 - remove for loop that did nothing

Pull Request - State: closed - Opened by npklein over 7 years ago

#617 - fixed small bug

Pull Request - State: closed - Opened by freerkvandijk over 7 years ago

#616 - readd old parameters

Pull Request - State: closed - Opened by npklein over 7 years ago

#614 - Updated genelist to use for job generation

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#613 - bugfix

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#612 - extra check if file exists otherwise error message is bad

Pull Request - State: closed - Opened by npklein almost 8 years ago

#611 - remove hard coded filepath

Pull Request - State: closed - Opened by npklein almost 8 years ago

#610 - include extra scripts in install script rasqual

Pull Request - State: closed - Opened by npklein almost 8 years ago

#609 - Small bugfix

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#608 - Updates on ASE pipeline

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#607 - add extra slash

Pull Request - State: closed - Opened by npklein almost 8 years ago

#605 - remove getFile putFile, change ReadbackPhasing for update

Pull Request - State: closed - Opened by npklein almost 8 years ago

#604 - Added rasqual install scirpt

Pull Request - State: closed - Opened by npklein almost 8 years ago

#603 - Bugfixes and added file (un)packing

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#602 - Remove getFile/putFile

Pull Request - State: closed - Opened by npklein almost 8 years ago

#601 - Removed getFile and putFile functions from protocols

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#600 - Removed --threshold option, see https://www.jiscmail.ac.uk/cgi-bin/we…

Pull Request - State: closed - Opened by npklein almost 8 years ago

#599 - ShapeitPhasing in chunks

Pull Request - State: closed - Opened by npklein almost 8 years ago

#598 - Changes to ASE pipeline to include running on meta-exon level

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago - 1 comment

#597 - EasyBuild version of ShapeitTools, fix of ligateHAPLOTYPES

Pull Request - State: closed - Opened by npklein almost 8 years ago

#596 - fixed wrong variable names and missing brackets

Pull Request - State: closed - Opened by npklein almost 8 years ago

#595 - Shapeit on chromsome chunks

Pull Request - State: closed - Opened by npklein almost 8 years ago

#594 - Small updates

Pull Request - State: closed - Opened by freerkvandijk almost 8 years ago

#593 - Two small bugfixes in ASE rasqual pipeline

Pull Request - State: closed - Opened by freerkvandijk about 8 years ago

#592 - Improved parallellization of ASE pipeline

Pull Request - State: closed - Opened by freerkvandijk about 8 years ago

#591 - Updates to enhance performance of ASE Rasqual pipeline

Pull Request - State: closed - Opened by freerkvandijk about 8 years ago

#590 - Fully functioning ASE pipeline using Rasqual

Pull Request - State: closed - Opened by freerkvandijk about 8 years ago - 1 comment

#589 - remove weird folder

Pull Request - State: closed - Opened by npklein about 8 years ago

#588 - updated generate_template NIPT for use on zinc-finger

Pull Request - State: closed - Opened by BenjaminsM about 8 years ago

#587 - Changed parameters for use on zinc-finger

Pull Request - State: closed - Opened by BenjaminsM about 8 years ago

#586 - GCCXX error fix, use gzipped vcf (phasing pipeline)

Pull Request - State: closed - Opened by npklein about 8 years ago

#585 - bugfixes

Pull Request - State: closed - Opened by RoanKanninga about 8 years ago

#584 - exit when failing

Pull Request - State: closed - Opened by npklein about 8 years ago

#583 - fix haplotypeCaller

Pull Request - State: closed - Opened by npklein about 8 years ago

#582 - upgrade to NGS_DNA-3.2.5

Pull Request - State: closed - Opened by RoanKanninga about 8 years ago

#581 - add #string haplotyperTargets

Pull Request - State: closed - Opened by npklein about 8 years ago - 1 comment

#580 - fix when there is no error or finished file

Pull Request - State: closed - Opened by RoanKanninga about 8 years ago

#579 - auto pipeline updates

Pull Request - State: closed - Opened by RoanKanninga about 8 years ago

#578 - move md5sums checked to logs instead of inside rawdata folder

Issue - State: open - Opened by RoanKanninga about 8 years ago
Labels: bug, NGS_Automated

#577 - add example generate jobs script

Pull Request - State: closed - Opened by npklein over 8 years ago

#576 - Created a GetSubreadCounts to count with featureCounts, modified the …

Pull Request - State: closed - Opened by CGUTA over 8 years ago

#575 - fix to early copy project data to prm trigger

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#574 - upgrade to NGS_DNA/3.2.4 + bugfixing

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#573 - fix issue that dataCopiedToPrm file is not created

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#572 - Delete generateMergeGenotypeGvcfJobsV3.pl

Pull Request - State: closed - Opened by npklein over 8 years ago

#571 - do ASReads and ASE per chromosome

Pull Request - State: closed - Opened by npklein over 8 years ago

#570 - Fixed hardcoded bug

Pull Request - State: closed - Opened by freerkvandijk over 8 years ago

#569 - putting rawdata logs in the per rawdata folder

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#568 - small changes to copyRawDataToPrm.sh

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#566 - Quick fix stupid error

Pull Request - State: closed - Opened by npklein over 8 years ago

#565 - Make HtseqCount work

Pull Request - State: closed - Opened by npklein over 8 years ago

#564 - fix

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#563 - exit with error if .sam file does not exist

Pull Request - State: closed - Opened by npklein over 8 years ago

#562 - fix error when rnastrandedness = unstranded

Pull Request - State: closed - Opened by npklein over 8 years ago

#561 - fixed error when secon fq file not present

Pull Request - State: closed - Opened by npklein over 8 years ago

#560 - Update prepare_Public_RNA-seq_QC.sh

Pull Request - State: closed - Opened by Bonder-MJ over 8 years ago

#559 - fix

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#558 - fix

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#557 - bugfix

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#556 - Updated NIPT Parameters.csv for use on leucine-zipper

Pull Request - State: closed - Opened by BenjaminsM over 8 years ago

#554 - added leucine-zipper parameters

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#553 - fix exclude path

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#543 - Not able te cleanup Zinc-finger rawdata/ngs

Issue - State: closed - Opened by Gerbenvandervries over 8 years ago - 1 comment
Labels: bug, NGS_Automated

#505 - Read count loglifes are not copied to permanent storage

Issue - State: closed - Opened by Gerbenvandervries over 8 years ago - 1 comment
Labels: bug, NGS_Demultiplex

#485 - Quality by cycle metrics calculation needed?

Issue - State: closed - Opened by RoanKanninga over 8 years ago - 1 comment
Labels: enhancement, NGS_DNA

#476 - Use Cram conversion for storing bam files

Issue - State: closed - Opened by RoanKanninga over 8 years ago - 1 comment
Labels: enhancement, NGS_DNA, NGS_RNA

#475 - Store g.vcf as g.vcf.gz

Issue - State: closed - Opened by RoanKanninga over 8 years ago - 1 comment
Labels: enhancement, NGS_DNA, NGS_RNA

#474 - Mail when error occurs during demultiplexing

Issue - State: closed - Opened by BenjaminsM over 8 years ago - 1 comment
Labels: enhancement, NGS_Demultiplex

#443 - QC report also in pdf format

Issue - State: closed - Opened by RoanKanninga over 8 years ago - 1 comment
Labels: enhancement, NGS_DNA

#441 - Fix pictures in the QC report

Issue - State: closed - Opened by RoanKanninga over 8 years ago
Labels: bug, NGS_DNA

#438 - Fix Demultiplex writing tmp_Demultiplex directory in results folder

Issue - State: closed - Opened by RoanKanninga over 8 years ago
Labels: bug, NGS_Demultiplex

#408 - Add --alleles option to UnifiedGenotyper in RNAseq pipeline

Issue - State: closed - Opened by npklein almost 9 years ago