nf-core/sarek issues and pull requests

#1383 - Fix `--three_prime_clip_r{1,2}` parameter documentation (fixes #1382)

Pull Request - State: open - Opened by tdanhorn 5 months ago - 3 comments

#1382 - Typo in `--three_prime_clip_r{1,2}` parameter documentation

Issue - State: open - Opened by tdanhorn 5 months ago
Labels: bug

#1381 - Ngscheckmate fix

Pull Request - State: closed - Opened by SPPearce 5 months ago - 3 comments

#1380 - Restart the Sentieon Test license server

Issue - State: open - Opened by maxulysse 5 months ago

#1379 - Run BAM QC after alignment

Issue - State: open - Opened by Matteodigg 6 months ago
Labels: enhancement

#1378 - Improve cloud testing matrix strategy

Pull Request - State: open - Opened by adamrtalbot 6 months ago - 6 comments

#1377 - bwamem2 indexing resources

Issue - State: open - Opened by Matteodigg 6 months ago
Labels: bug

#1376 - control-freec throws an error when running WES data in tumor-only mode because parameter minimalsubclonepresence is set

Issue - State: open - Opened by rgraus 6 months ago
Labels: bug

#1375 - improve documentation to point out that when using ASCAT and the Format in the BAM file is chr, one has to change the loci ascat reference file to be also in the chr format

Issue - State: open - Opened by rgraus 6 months ago
Labels: bug

#1374 - Change job name in cloudtest.yml

Pull Request - State: closed - Opened by adamrtalbot 6 months ago - 2 comments

#1373 - fix intervals file

Pull Request - State: closed - Opened by FriederikeHanssen 6 months ago - 1 comment

#1372 - Add test profile for ncbench

Pull Request - State: closed - Opened by FriederikeHanssen 6 months ago - 2 comments

#1371 - Not valid SNP_GRCh38_hg38_wChr.bed on GATK.GRCh38

Issue - State: open - Opened by jbague 6 months ago - 10 comments
Labels: bug

#1370 - Adapting nf-core/sarek for Ion Torrent Single-End Data Analysis

Issue - State: closed - Opened by Sadiki-Noureddine 6 months ago - 2 comments
Labels: bug

#1369 - Mutect2 error with Sarek 3.4.0

Issue - State: open - Opened by mimifp 6 months ago - 4 comments
Labels: bug

#1368 - Sambamba

Pull Request - State: open - Opened by stavgrossfeld 6 months ago - 2 comments

#1367 - sambamba/markdup

Issue - State: open - Opened by stavgrossfeld 6 months ago - 1 comment
Labels: enhancement

#1366 - NGSCHECKMATE_NCM

Issue - State: open - Opened by LuciaNhuNguyen 6 months ago - 6 comments
Labels: enhancement

#1365 - Template update for nf-core/tools version 2.11.1

Pull Request - State: closed - Opened by mirpedrol 6 months ago - 3 comments

#1364 - 1357 grouping strategy applied by counting number of FASTQ files generated by FASTP

Pull Request - State: closed - Opened by adamrtalbot 6 months ago - 5 comments

#1363 - Minimum split_fastq value is 250

Issue - State: closed - Opened by adamrtalbot 7 months ago - 4 comments
Labels: bug

#1362 - Check docker.runOptions for spark

Issue - State: open - Opened by maxulysse 7 months ago

#1361 - Increase run time

Issue - State: closed - Opened by gitMakeCoffee 7 months ago - 3 comments
Labels: bug

#1360 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 7 months ago - 1 comment

#1359 - remove params from subworkflows

Pull Request - State: closed - Opened by maxulysse 7 months ago - 2 comments

#1358 - Replace DRAGMAP with NARFMAP

Pull Request - State: open - Opened by edmundmiller 7 months ago - 4 comments

#1357 - Large discrepancy between number of reads in the same sample but in different lanes causes a sample to get dropped

Issue - State: closed - Opened by adamrtalbot 7 months ago - 3 comments
Labels: bug

#1356 - ngscheckmate_bed is set incorrectly for GATK.GRCh37

Issue - State: open - Opened by SPPearce 7 months ago
Labels: bug

#1355 - Allow to specify a local config file for snpEff

Issue - State: open - Opened by maxulysse 7 months ago
Labels: enhancement

#1354 - Allow for snpEff db without versions

Issue - State: open - Opened by maxulysse 7 months ago
Labels: enhancement

#1353 - use utils subworkflows

Pull Request - State: open - Opened by maxulysse 7 months ago - 1 comment

#1352 - Strelka malformed VCF header

Issue - State: closed - Opened by gitMakeCoffee 7 months ago - 3 comments
Labels: bug

#1351 - fix params in test profiles

Pull Request - State: closed - Opened by maxulysse 7 months ago - 2 comments

#1350 - update Dragmap

Pull Request - State: closed - Opened by maxulysse 7 months ago - 7 comments

#1349 - Fix nf-tests coming from nf-core/modules

Issue - State: open - Opened by maxulysse 7 months ago

#1348 - Unpatch dragmap modules

Issue - State: open - Opened by maxulysse 7 months ago

#1347 - Error while FASTP is running

Issue - State: closed - Opened by cuppacuppa 7 months ago - 6 comments

#1346 - No parameter for "penalty" in ASCAT segmentation

Issue - State: open - Opened by MGCarta 7 months ago - 1 comment
Labels: enhancement

#1345 - Preserve STDERR

Pull Request - State: closed - Opened by sminot 7 months ago - 2 comments

#1344 - enable qc when starting from VC

Pull Request - State: closed - Opened by FriederikeHanssen 7 months ago - 2 comments

#1343 - Paper review

Pull Request - State: closed - Opened by FriederikeHanssen 7 months ago - 1 comment

#1342 - VEP on Strelka indel output

Issue - State: closed - Opened by frenkiboy 7 months ago - 1 comment
Labels: question

#1341 - sarek on Kubernetes documentation

Issue - State: closed - Opened by radaniba 7 months ago - 1 comment
Labels: enhancement

#1340 - Add Azure megatests

Pull Request - State: closed - Opened by adamrtalbot 7 months ago - 19 comments

#1339 - Update sentieon-modules

Pull Request - State: closed - Opened by asp8200 7 months ago - 1 comment

#1338 - switch to using --write-index instead of samtools index

Pull Request - State: open - Opened by FriederikeHanssen 7 months ago - 3 comments

#1337 - Validate that only vcf.gz(.tbi) are provided

Issue - State: open - Opened by FriederikeHanssen 8 months ago
Labels: enhancement, input validation

#1336 - Annotations for custom genome

Issue - State: closed - Opened by rakesh-res 8 months ago - 2 comments
Labels: question

#1335 - add docs for bcftools annotate params

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 6 comments

#1334 - remove extra v for slack report

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 1 comment

#1333 - Back to Dev

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 2 comments

#1332 - Java applications request too much memory

Issue - State: open - Opened by rrlove-cdc 8 months ago
Labels: bug

#1331 - Add nf-test scatter CI testing

Issue - State: open - Opened by Emiller88 8 months ago
Labels: testing

#1330 - Add SnpEff to full sized tests

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 1 comment

#1329 - haplotypecaller output unusual behavior without dbsnps/known-sites

Issue - State: open - Opened by AJTDaedalus 8 months ago
Labels: bug

#1328 - Fix links to docs

Pull Request - State: closed - Opened by maxulysse 8 months ago - 1 comment

#1327 - Update all modules to have environment name

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 6 comments

#1326 - Misleading info in error message concerning invalid path to VEP-cache

Issue - State: open - Opened by asp8200 8 months ago - 3 comments
Labels: bug

#1325 - Update config files and other minor code polishing

Pull Request - State: closed - Opened by maxulysse 8 months ago - 6 comments

#1324 - Address code reviews from #1320

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 1 comment

#1323 - Error with ASCAT

Issue - State: open - Opened by TuongViDang 8 months ago - 3 comments
Labels: bug

#1322 - How to output allele-specific copy number in CNVkit?

Issue - State: open - Opened by TuongViDang 8 months ago
Labels: enhancement

#1321 - ACTUAL Release 3.4

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 4 comments

#1320 - [DON' MERGE] Release 3.4.0

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 6 comments

#1319 - Bump version, set release names

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 1 comment

#1318 - fix issues with params json dump

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 3 comments

#1317 - update subway map

Pull Request - State: closed - Opened by FriederikeHanssen 8 months ago - 1 comment

#1316 - Fix UMI-link

Issue - State: open - Opened by asp8200 8 months ago
Labels: bug

#1315 - Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows

Pull Request - State: closed - Opened by asp8200 8 months ago - 2 comments

#1314 - When both sentieon_haplotype and haplotypecaller are provided, config scopes are clashing

Issue - State: closed - Opened by FriederikeHanssen 8 months ago - 3 comments
Labels: bug

#1313 - Sarek stops after alignment and does not perform variant calling

Issue - State: closed - Opened by sci-kai 8 months ago - 16 comments
Labels: bug

#1312 - implementation of goleft/indexcov

Pull Request - State: open - Opened by lindenb 8 months ago - 3 comments

#1311 - update local modules

Pull Request - State: closed - Opened by maxulysse 8 months ago - 1 comment

#1309 - try better empty channel management for germline ressource in mutect2 subworkflow

Pull Request - State: closed - Opened by maxulysse 8 months ago - 2 comments

#1308 - Be consistent with the meta map for the reference files

Issue - State: open - Opened by maxulysse 8 months ago

#1306 - Strelka requires `.crai` files to match format `PREFIX.cram.crai`

Issue - State: open - Opened by awgymer 8 months ago
Labels: bug, input validation

#1304 - CHORES: update all modules

Pull Request - State: closed - Opened by maxulysse 8 months ago - 4 comments

#1303 - FEAT: Proper usage of vep_version

Pull Request - State: closed - Opened by maxulysse 8 months ago - 2 comments

#1302 - Fixing versions of nf-plugins

Pull Request - State: closed - Opened by asp8200 8 months ago - 4 comments

#1301 - FIX: nf-prov usage

Pull Request - State: closed - Opened by maxulysse 8 months ago - 4 comments

#1300 - Fix the version of the plugins used in Sarek

Issue - State: closed - Opened by asp8200 8 months ago
Labels: enhancement

#1299 - Config setting `prov.formats`

Issue - State: closed - Opened by LuciaNhuNguyen 8 months ago - 12 comments
Labels: bug

#1298 - FIX: Remove use_annotation_cache_keys params

Pull Request - State: closed - Opened by maxulysse 8 months ago - 5 comments

#1297 - Sarek --download_cache does not work properly

Issue - State: closed - Opened by Hadi90Eidgah 8 months ago - 5 comments
Labels: bug

#1296 - ContaminationAssessment in the Sentieon-subworkflows TNseq and TNscope?

Issue - State: open - Opened by asp8200 8 months ago
Labels: enhancement

#1295 - Sarek stops and cannot connect to amazonaws

Issue - State: open - Opened by vmelichar 8 months ago - 1 comment
Labels: bug

#1294 - Change vep_version to vep_cache_version in ENSEMBLVEP_VEP-config

Pull Request - State: closed - Opened by asp8200 8 months ago - 3 comments

#1293 - Samplesheets with more normal-samples per patient pass nf-validation

Issue - State: open - Opened by asp8200 8 months ago
Labels: bug, input validation

#1292 - CNVKIT - Export cns file into seg format for IGV

Issue - State: open - Opened by maxulysse 9 months ago

#1291 - Fix CODEOWNERS

Pull Request - State: closed - Opened by Emiller88 9 months ago - 1 comment

#1290 - minor nf test fixes

Pull Request - State: closed - Opened by adamrtalbot 9 months ago - 1 comment

#1289 - separate pytest from nftest

Pull Request - State: closed - Opened by adamrtalbot 9 months ago - 2 comments

#1288 - Add an nf-test CI

Pull Request - State: closed - Opened by adamrtalbot 9 months ago - 2 comments

#1287 - Adding labels to the local modules

Pull Request - State: closed - Opened by asp8200 9 months ago - 3 comments

#1286 - Created subworkflow for parsing samplesheet with nf-test

Pull Request - State: closed - Opened by RaqManzano 9 months ago - 5 comments
Labels: enhancement

#1285 - new subworkflow: samplesheet handling

Issue - State: open - Opened by RaqManzano 9 months ago - 1 comment
Labels: enhancement

#1284 - Switch to nf-core/fastq_create_umi_consensus_fgbio subworkflow

Pull Request - State: closed - Opened by berguner 9 months ago - 1 comment

#1283 - Usage.md: link to example samplesheet is broken

Issue - State: open - Opened by FriederikeHanssen 9 months ago
Labels: bug

#1282 - The pipeline should fail early when --no_intervals is used with joint germline calling

Issue - State: open - Opened by FriederikeHanssen 9 months ago - 3 comments
Labels: bug

#1281 - Readme uses bith light and dark logo at all times

Issue - State: open - Opened by FriederikeHanssen 9 months ago
Labels: bug

GitHub / nf-core/sarek issues and pull requests