nf-core/raredisease issues and pull requests

#439 - Document which variant catalogs to use for expansionhunter-stranger

Issue - State: open - Opened by jemten about 1 year ago
Labels: documentation

#438 - skip haplocheck and fastqc [skip ci]

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

#437 - SMN copy number caller crashes due to mismatched reference genome

Issue - State: open - Opened by Jakob37 about 1 year ago - 3 comments
Labels: bug

#436 - add skip_qualimap and skip_eklipse parameters

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

#435 - fix warnings and clean up terminal logs

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

#434 - Add cnvnator subworkflow

Pull Request - State: open - Opened by ramprasadn about 1 year ago - 1 comment

#433 - Add cnvnator

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

#432 - Add logo+metromap for both light and dark themes

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

#431 - Template updates v2.10

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

#430 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#429 - Four individuals, two affected by phenotype, rhocall annotate problem

Issue - State: open - Opened by fa2k about 1 year ago - 6 comments
Labels: bug

#428 - add metromap with core elements

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

#427 - DeepMind AlphaMissense

Issue - State: open - Opened by dnil about 1 year ago
Labels: enhancement

#426 - GENMOD and missing values on master

Issue - State: open - Opened by lfearnley about 1 year ago
Labels: bug

#425 - Add a new sample field to meta

Pull Request - State: closed - Opened by ramprasadn about 1 year ago - 4 comments

#424 - Add BPHunter

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

#423 - Metro map

Pull Request - State: closed - Opened by hrydbeck about 1 year ago - 6 comments

#422 - Update dnascope-module

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#419 - Refactor mitochondrial analysis workflow

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

#418 - BCFTOOLS ROH and multiple lanes - sample names duplicated in command

Issue - State: open - Opened by lfearnley about 1 year ago
Labels: bug

#417 - Sample names - reserved characters?

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

#416 - Add skip_vep_filter parameter

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

#415 - Implement GATK-gCNV tool for CNV detection

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

#414 - Provide information on which software needs which input file

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

#413 - nf-raredisease crashing on filter_vep

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

#412 - Update modules to their latest nf-core version

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

#411 - Set "0" a default for missing maternal and paternal id in ped file

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

#410 - Fill in "0" for missing information in ped file

Issue - State: closed - Opened by jemten over 1 year ago - 1 comment
Labels: bug, Effort low

#409 - Update modules to their latest nf-core version

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

#408 - Modules update

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

#407 - CADD container image with dependencies included

Issue - State: open - Opened by fa2k over 1 year ago - 1 comment
Labels: enhancement

#406 - Add sentieon/dnascope from nf-core/modules

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

#405 - Number of ENSEMBLVEP_SNV instances when using CADD

Issue - State: open - Opened by fa2k over 1 year ago
Labels: bug

#404 - Replace local version of SENTIEON_WGSMETRICS with nf-core version

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#403 - Replace local version of SENTIEON_DNAMODELAPPLY with nf-core version

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#402 - Remove sentieon BQSR

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#401 - Replace local version of sentieon-locuscollector and sentieon-dedup

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#400 - Replace local version of SENTIEON_DATAMETRICS with nf-core version

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#399 - Replace local version of SENTIEON_READWRITER with nf-core version

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#398 - Installing and calling nf-core/modules version of sentieon/bwamem

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#397 - Update sentieon bwamemindex

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 2 comments

#396 - Add constraints to block the pipeline from running CollectWgsMetrics on WES samples

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

#395 - Make target bed file optional for WGS mode

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

#394 - Update documentation

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

#393 - sort ranked SVs before indexing

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 13 comments

#392 - Make cram prefix same as the default markduplicates prefix

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

#391 - Correct GATK4 container spec

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

#390 - Sync dev to latest master with changes from patch release 1.1.1

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

#389 - Add documentation for running without Internet access

Pull Request - State: closed - Opened by fa2k over 1 year ago - 4 comments

#388 - Patch release v1.1.1

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

#387 - nf-validation makes it difficult to run without Internet access

Issue - State: closed - Opened by fa2k over 1 year ago - 2 comments
Labels: bug

#386 - switch to nf-validation for parameter and samplesheet validation

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

#385 - Updating tiddit to v3.6.1

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#384 - bumpversion to 1.2.0dev

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

#383 - Multiple entry points: add BAM inputs

Pull Request - State: open - Opened by fa2k over 1 year ago - 1 comment

#382 - review suggestions release prep v1.1.0

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

#381 - SV ranked variants Chromosome blocks not continuous

Issue - State: closed - Opened by fa2k over 1 year ago
Labels: bug

#380 - Documentation - variant_catalog is for Stranger, not ExpansionHunter

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

#379 - Default memory allocations for bwa index step are too low for igenomes

Issue - State: closed - Opened by lfearnley over 1 year ago - 4 comments
Labels: bug

#378 - KeyError: 'X' at Tiddit stage

Issue - State: closed - Opened by hrydbeck over 1 year ago - 9 comments
Labels: bug

#377 - Release v1.1.0

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

#376 - Release prep v1.1.0

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

#375 - Pipeline in WGS mode appears to require target_bed

Issue - State: closed - Opened by lfearnley over 1 year ago - 8 comments
Labels: bug

#374 - update eklipse

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

#373 - Update schema, output.md, and remove unused parameters

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

#372 - Update to template 2.9

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

#371 - update modules

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

#370 - MT workflow not compatible with genmod scoring

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

#369 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#368 - Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 1 comment

#367 - Missed collect-file cache

Issue - State: closed - Opened by hrydbeck over 1 year ago - 1 comment
Labels: bug

#366 - add chromograph

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

#365 - Add ek

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

#364 - Adding upd

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

#363 - Update case info

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

#362 - Gatkcnvcaller

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

#361 - Merge devplaceholder to dev

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

#360 - Add_public_aws_ecr_profile

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

#359 - update doi

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

#358 - Bumpversion on dev

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

#357 - added check for case id

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

#356 - Change VEP cache parameter description

Pull Request - State: closed - Opened by fa2k over 1 year ago - 1 comment

#355 - feat added hmtnote annotation

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

#354 - Add shiftfasta

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

#353 - Documentation - Mandatory options for SNV annotation

Pull Request - State: closed - Opened by fa2k over 1 year ago - 4 comments

#352 - rename channels

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

#351 - score_config_snv is mandatory

Issue - State: closed - Opened by fa2k over 1 year ago - 2 comments
Labels: bug

#350 - Update modules

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

#349 - feat added MT deletion script

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

#348 - Review suggestions

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

#347 - Add MT deletion script equivalent to the one in MIP

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

#346 - review suggestions

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

#345 - Review suggestions

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

#344 - smn_caller.py: error: argument --prefix: expected one argument

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

#343 - Modules update

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

#342 - Wes fixes in configs and subworkflows

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

#341 - Introduce checks for mandatory parameters

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

#340 - convert bam to cram

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

#339 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#338 - Mores updates from review suggestions

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

GitHub / nf-core/raredisease issues and pull requests