nf-core/raredisease issues and pull requests

#337 - Stability & performance improvements

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#336 - Fix documentation review comments release

Pull Request - State: closed - Opened by peterpru over 1 year ago - 1 comment

#335 - move code in make_ped.nf to raredisease.nf

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#334 - Missing `fromPath` parameter

Issue - State: closed - Opened by chels0 over 1 year ago - 15 comments
Labels: bug

#333 - fix: No such variable: case_info

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#332 - No such variable: case_info

Issue - State: closed - Opened by chels0 over 1 year ago - 2 comments
Labels: bug

#331 - Add GATKs CNVcaller

Issue - State: closed - Opened by ramprasadn over 1 year ago - 1 comment
Labels: enhancement, Impact high, Effort high, Priority high

#330 - remove stub in ci.yml

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 2 comments

#329 - Calling mobile elements

Issue - State: open - Opened by jemten over 1 year ago - 1 comment
Labels: enhancement, Impact high, Effort medium, Priority medium

#328 - UPD calling

Issue - State: closed - Opened by jemten over 1 year ago
Labels: enhancement

#327 - Compress bam to cram

Issue - State: closed - Opened by jemten over 1 year ago
Labels: enhancement, Impact low, Effort low, Priority high

#326 - Add eKLIPse to MT workflow

Issue - State: closed - Opened by Lucpen over 1 year ago - 1 comment
Labels: enhancement

#325 - Annotate small indels with CADD scores

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#324 - Update peddy config

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#323 - Minor fixes and improvements

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 2 comments

#322 - Release 1.0.0

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 7 comments

#321 - Documentation

Pull Request - State: closed - Opened by Gwennid over 1 year ago - 2 comments

#320 - Release 1.0.0dev

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 9 comments

#319 - Move haplocheck outside of align_and_call_MT subworkflow?

Issue - State: closed - Opened by ramprasadn over 1 year ago
Labels: enhancement, Impact low, Effort medium, Priority medium

#318 - Customize aws full pipeline tests

Issue - State: open - Opened by ramprasadn over 1 year ago
Labels: enhancement

#317 - Add citation for the pipeline after first release

Issue - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#316 - Add full sized test dataset

Issue - State: open - Opened by ramprasadn over 1 year ago
Labels: enhancement

#315 - Update meta.readgroups

Issue - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#314 - Fix lint warnings and modules update

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#313 - Output md

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#312 - Update multiqc reporting

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#311 - Update according to nf-core pipeline guidelines

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#310 - update README.md

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#309 - Update CITATIONS.md

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#308 - compress and index vcf outputs

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#307 - Publish files

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#306 - Refactor subworkflows

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#305 - remvoe unused pipeline parameters and variables in subworkflows

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#304 - Simplify ternary operators in the raredisease workflow

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#303 - Usagedocs

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 2 comments

#302 - Add bam qc to multiqc

Pull Request - State: closed - Opened by peterpru over 1 year ago - 3 comments
Labels: ready for review

#301 - merge expansionhunter calls

Pull Request - State: closed - Opened by jemten over 1 year ago - 2 comments
Labels: ready for review

#300 - update smncopynumbercaller

Pull Request - State: closed - Opened by peterpru over 1 year ago - 1 comment

#299 - removes unused process from modules config

Pull Request - State: closed - Opened by jemten over 1 year ago - 1 comment

#298 - Collect qc report for multiqc

Issue - State: closed - Opened by jemten over 1 year ago - 3 comments

#297 - break modules.config into smaller configs

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 2 comments

#296 - Update Peddy module on nfcore repo

Issue - State: closed - Opened by sima-r over 1 year ago - 1 comment
Labels: ready for review, nf-core/modules

#295 - Refactor modules.config

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#294 - Updates for sentieon modules

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 3 comments
Labels: ready for review

#293 - more fixes for the test profile

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#292 - Rename fix

Pull Request - State: closed - Opened by jemten over 1 year ago - 1 comment

#291 - Update configs

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#290 - Final add vcfanno mt

Pull Request - State: closed - Opened by Lucpen over 1 year ago - 1 comment
Labels: ready for review

#289 - Mt anno 2

Pull Request - State: closed - Opened by Lucpen over 1 year ago - 1 comment

#288 - Update files for collectwgsmetrics

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#287 - Remove null from version ch

Pull Request - State: closed - Opened by jemten over 1 year ago - 1 comment

#286 - Update tests

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment

#285 - Peddy backup

Pull Request - State: closed - Opened by sima-r over 1 year ago - 1 comment

#284 - updates modules to remove enable_conda

Pull Request - State: closed - Opened by jemten over 1 year ago - 1 comment

#279 - Peddy

Pull Request - State: closed - Opened by sima-r over 1 year ago - 3 comments

#276 - Vcf anno mt

Pull Request - State: closed - Opened by Lucpen over 1 year ago - 4 comments
Labels: WIP

#273 - Update modules to latest version

Issue - State: closed - Opened by jemten almost 2 years ago - 1 comment

#270 - Add SMNCopyNumberCaller to raredisease

Pull Request - State: closed - Opened by peterpru almost 2 years ago - 2 comments
Labels: ready for review

#269 - feat added gnomad annotation to VEP for MT

Pull Request - State: closed - Opened by Lucpen almost 2 years ago - 2 comments
Labels: WIP

#268 - feat updated MT subworkflow

Pull Request - State: closed - Opened by Lucpen almost 2 years ago
Labels: WIP

#266 - review suggestions

Pull Request - State: closed - Opened by ramprasadn almost 2 years ago - 1 comment

#261 - Add more entry points to the workflow

Issue - State: open - Opened by ramprasadn almost 2 years ago - 4 comments
Labels: enhancement, Impact high, Effort high, Priority medium

#258 - combine calls from mitochondrial and snv variant calling subworflows

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

#254 - Add Gatk4 GermlineCNVCaller modules and subworkflow

Pull Request - State: closed - Opened by ryanjameskennedy almost 2 years ago - 5 comments
Labels: help wanted, nf-core/modules

#253 - Don't use a process to rename a file

Issue - State: closed - Opened by jemten almost 2 years ago - 1 comment

#246 - Add SMNCopyNumberCaller

Issue - State: closed - Opened by jemten almost 2 years ago
Labels: enhancement

#243 - generate compressed vcf outputs

Issue - State: open - Opened by ramprasadn almost 2 years ago - 19 comments
Labels: enhancement

#237 - Check pedigree files

Issue - State: closed - Opened by ramprasadn almost 2 years ago - 1 comment

#230 - Last mt sw

Pull Request - State: closed - Opened by Lucpen almost 2 years ago - 2 comments
Labels: WIP

#227 - split multiallelics and merge expansionhunter calls

Issue - State: closed - Opened by jemten almost 2 years ago - 1 comment

#189 - GATK4 nf-core containers lacking package (gcnvkernel) required for the gcnvcaller

Issue - State: closed - Opened by ryanjameskennedy over 2 years ago - 1 comment
Labels: WIP, nf-core/modules

#187 - Sbwkflw mapping mt

Pull Request - State: closed - Opened by Lucpen over 2 years ago - 1 comment
Labels: ready for review, subworkflow

#185 - Add check for case_id

Issue - State: closed - Opened by jemten over 2 years ago - 2 comments
Labels: enhancement

#184 - Add bcftools filter

Issue - State: closed - Opened by sima-r over 2 years ago - 1 comment

#182 - vcfanno_resources Argument of `file` function cannot be empty

Issue - State: closed - Opened by barissalman over 2 years ago - 2 comments
Labels: bug

#173 - rm local_config_path param and refactor

Pull Request - State: closed - Opened by projectoriented over 2 years ago - 2 comments

#164 - Peddy

Issue - State: closed - Opened by EmmaCAndersson over 2 years ago - 1 comment
Labels: nf-core/modules

#155 - HmtNote

Issue - State: closed - Opened by sysbiocoder over 2 years ago - 1 comment
Labels: enhancement

#147 - Make a "metromap" for the pipeline

Issue - State: closed - Opened by Gwennid over 2 years ago - 1 comment
Labels: enhancement

#143 - Add CADD for indels

Issue - State: closed - Opened by jemten over 2 years ago - 5 comments
Labels: enhancement

#137 - Update resource request in usage.md

Issue - State: closed - Opened by jemten over 2 years ago - 2 comments
Labels: documentation

#134 - Step by step tutorial -Mitochondria pipeline

Issue - State: closed - Opened by sysbiocoder over 2 years ago - 1 comment
Labels: enhancement

#120 - What to expect from the pipeline?

Issue - State: closed - Opened by projectoriented over 2 years ago - 2 comments
Labels: documentation

#116 - Filter black list regions

Issue - State: closed - Opened by sysbiocoder over 2 years ago - 2 comments
Labels: enhancement

#109 - How-to update the pipeline flowchart

Issue - State: closed - Opened by Gwennid over 2 years ago - 1 comment
Labels: documentation

#48 - Mitochondria workflow

Issue - State: closed - Opened by Gwennid almost 3 years ago - 20 comments
Labels: enhancement

#3 - Add test dataset to enable CI tests

Issue - State: closed - Opened by henrikstranneheim over 3 years ago - 2 comments
Labels: enhancement

#1 - Draft overview of future pipeline

Issue - State: closed - Opened by jemten over 3 years ago
Labels: enhancement

GitHub / nf-core/raredisease issues and pull requests