mskcc/tempo issues and pull requests

#99 - Update pipeline chart to include germline work

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 2 comments
Labels: enhancement

#98 - implement mutational signatures in NF

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 9 comments
Labels: enhancement

#97 - Release 0.5.0

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

#96 - Revert "Feature/somatic workflow changes"

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

#95 - Feature/reference

Pull Request - State: closed - Opened by gongyixiao almost 6 years ago - 1 comment
Labels: enhancement

#94 - Feature/reference

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

#93 - Alfred ReadGroup ignore

Pull Request - State: closed - Opened by sivkovic almost 6 years ago - 1 comment

#92 - Make more informative travis-CI tests

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 2 comments
Labels: enhancement

#91 - How to get file sizes and other metadata from Nextflow runs

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 8 comments
Labels: question, nextflow

#90 - HLA Polysolver

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 8 comments
Labels: enhancement

#89 - Feature/somatic workflow changes

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

#88 - Feature/refactor mutect2

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 2 comments
Labels: enhancement

#87 - Hard-setting gatk to version 4.1.0.0 because of errors

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#86 - Removed makeSampleFile process; placed logic directly in delly filter

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#85 - Discuss germline.nf

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 2 comments
Labels: enhancement

#84 - Feature/update readme

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#83 - Alfred Dockerfile

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

#82 - Fix permissions for EC2 Role

Pull Request - State: closed - Opened by sivkovic almost 6 years ago
Labels: bug

#81 - Remove makeSamplesFile process?

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 7 comments
Labels: question

#80 - Feature/fastqc fastp #25

Pull Request - State: closed - Opened by hweej almost 6 years ago - 3 comments
Labels: enhancement

#79 - Feature/vcf2maf

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#78 - Choose SV callers

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 2 comments
Labels: enhancement, help wanted

#77 - BAMQC at the RG and sample level

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#76 - Validate somatic.nf results on real data

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 3 comments
Labels: enhancement

#75 - DockerTimeout on AWS Batch

Issue - State: closed - Opened by sivkovic almost 6 years ago - 3 comments
Labels: bug

#74 - Release 0.4.0

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

#73 - Add somatic.nf tests for Travis-CI

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment
Labels: enhancement

#72 - Fixed delly bug; filter goes through all sv variants now

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#71 - Alfred

Pull Request - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#70 - Something to think about for germline, maybe: https://github.com/Illumina/canvas

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago
Labels: enhancement

#69 - vcf2maf of merged vcf files

Issue - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#68 - Feature/bcftools

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#67 - Autoscalling EBS

Pull Request - State: closed - Opened by sivkovic almost 6 years ago - 1 comment
Labels: enhancement

#66 - Feature/reformat somatic

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#65 - NF PR in order to fix memory issue

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 2 comments
Labels: bug, enhancement

#64 - Implement SV caller, NovoBreak

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 2 comments
Labels: enhancement, backburner

#63 - Implement SV caller, GRIDSS

Issue - State: open - Opened by evanbiederstedt almost 6 years ago - 5 comments
Labels: enhancement, high priority, somatic analysis

#62 - Finish QC steps for BAMs, using Alfred: https://github.com/tobiasrausch/alfred

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 1 comment
Labels: enhancement

#61 - Re-configure config files/infrastructure. Purge Sarek legacy code?

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 6 comments
Labels: enhancement

#60 - Finish FastQC

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 1 comment
Labels: enhancement

#59 - Implement a function which will split the FASTQ input if the FASTQ input is greater than a certain size.

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 3 comments
Labels: enhancement

#58 - Mutational Signatures: create a Docker image for this, and push to Dockerhub

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 6 comments
Labels: enhancement

#57 - Document provenance of reference files

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 4 comments
Labels: enhancement, question

#56 - Performance Enhancement for BAM preprocessing

Issue - State: closed - Opened by gongyixiao almost 6 years ago
Labels: enhancement

#55 - singularity image pull fails with "no descriptor found for reference" error

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 6 comments
Labels: bug, backburner

#54 - Implement Mark Duplicates before and after the merging of BAMs

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 3 comments
Labels: enhancement

#53 - Feature/pipe map reads

Pull Request - State: closed - Opened by gongyixiao almost 6 years ago - 3 comments
Labels: enhancement

#52 - Make a boolean flag to use BQSR or skip BQSR

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 1 comment
Labels: invalid

#51 - Feature/pipe map reads

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

#50 - Fix RG in bam

Pull Request - State: closed - Opened by kpjonsson almost 6 years ago - 2 comments
Labels: enhancement

#49 - Define sample sheet and pairing design

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 17 comments
Labels: enhancement

#48 - Release 0.3.0

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

#47 - Fixed configs

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

#46 - Implement interval file usage

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 8 comments
Labels: enhancement

#45 - Feature/mutect2 intervals bed

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#44 - Fix CreateRecalibrationTable bug

Pull Request - State: closed - Opened by kpjonsson almost 6 years ago
Labels: bug

#43 - Autoscale EBS for Amazon AMI

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#42 - Cleanup make_bam_and_qc.nf

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

#41 - Test travis

Pull Request - State: closed - Opened by nikhil almost 6 years ago
Labels: enhancement

#40 - Test travis

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

#39 - MarkDup .bai file

Issue - State: closed - Opened by gongyixiao almost 6 years ago - 1 comment
Labels: bug

#38 - Merge BAMs performance optimization

Issue - State: closed - Opened by sivkovic almost 6 years ago - 10 comments
Labels: enhancement

#37 - Feature/sample sheets

Pull Request - State: closed - Opened by gongyixiao almost 6 years ago
Labels: bug

#36 - hotfix/make bam and qc

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

#35 - "intervals" setting in reference file for WGS and WES need to be different, affecting BQSR

Issue - State: closed - Opened by gongyixiao almost 6 years ago - 10 comments
Labels: enhancement

#34 - Fix RG assignment in `AlignReads`

Issue - State: closed - Opened by kpjonsson almost 6 years ago - 11 comments
Labels: enhancement

#33 - Define WES and WGS example files to run through the pipeline scripts after every release

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 7 comments
Labels: enhancement

#32 - Memory reservation problems between Nextflow and JUNO LSF Cluster settings

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 7 comments
Labels: bug, backburner

#31 - -B option for bwa mem

Issue - State: closed - Opened by gongyixiao almost 6 years ago - 7 comments
Labels: enhancement, backburner

#30 - Updated readme to clarify computer environment name

Pull Request - State: closed - Opened by nikhil almost 6 years ago - 1 comment

#29 - Update README.md

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

#28 - Simplify container configs

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#27 - Implement interval bed for mutect2

Issue - State: closed - Opened by allanbolipata almost 6 years ago
Labels: enhancement

#26 - Release 0.2.0

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

#25 - Add QC for fastq and bam files in make_bam_and_qc.nf

Issue - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment
Labels: enhancement

#24 - feature/lumpyexpress added to somatic.nf

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#23 - Feature/ami build script

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

#22 - Error on juno when running with singularity from user home directory

Issue - State: closed - Opened by sivkovic almost 6 years ago - 10 comments
Labels: bug

#21 - Version 0.1.0

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

#20 - Feature/merge bams

Pull Request - State: closed - Opened by hweej almost 6 years ago - 1 comment
Labels: enhancement

#19 - Added sequenceType to test files, nextflow.config, and somatic.nf

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 2 comments

#18 - Feature/awsbatch readme

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

#17 - Tool conditional added with --tools flag

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

#16 - filtermutect2calls

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#15 - bcftools norm

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#14 - bcftools merge

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#13 - Lumpyexpress

Issue - State: closed - Opened by sivkovic almost 6 years ago

#12 - MSI sensor

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#11 - Finalize main_align_markDups_BaseRecal.nf to output (merged) BAMs with QC

Issue - State: closed - Opened by sivkovic almost 6 years ago - 3 comments
Labels: enhancement

#10 - Create AWS setup environment script

Issue - State: closed - Opened by sivkovic almost 6 years ago
Labels: enhancement

#9 - Update cmopipeline containers to work on AWS

Issue - State: closed - Opened by sivkovic almost 6 years ago - 1 comment
Labels: bug

#8 - Continuous Integration testing

Issue - State: closed - Opened by sivkovic almost 6 years ago - 1 comment
Labels: enhancement

#7 - feature/resource_refactor

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

#6 - delly, mutect2, manta, strelka2, facets added to somatic.nf

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 2 comments

#5 - Features - delly and mutect2

Pull Request - State: closed - Opened by allanbolipata almost 6 years ago - 1 comment

#4 - Merging develop to features/sv_callers

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

#3 - Feature/reference config refactor

Pull Request - State: closed - Opened by sivkovic almost 6 years ago - 1 comment

#2 - branched from nextflow_evan_awsbatch

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

#1 - Nextflow ToDo

Issue - State: closed - Opened by kpjonsson almost 6 years ago
Labels: nextflow

GitHub / mskcc/tempo issues and pull requests