Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / 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 8 months ago
- 3 comments
#1382 - Typo in `--three_prime_clip_r{1,2}` parameter documentation
Issue -
State: open - Opened by tdanhorn 8 months ago
Labels: bug
#1381 - Ngscheckmate fix
Pull Request -
State: closed - Opened by SPPearce 8 months ago
- 3 comments
#1380 - Restart the Sentieon Test license server
Issue -
State: open - Opened by maxulysse 8 months ago
#1379 - Run BAM QC after alignment
Issue -
State: open - Opened by Matteodigg 9 months ago
Labels: enhancement
#1378 - Improve cloud testing matrix strategy
Pull Request -
State: open - Opened by adamrtalbot 9 months ago
- 6 comments
#1377 - bwamem2 indexing resources
Issue -
State: open - Opened by Matteodigg 9 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 9 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 9 months ago
Labels: bug
#1374 - Change job name in cloudtest.yml
Pull Request -
State: closed - Opened by adamrtalbot 9 months ago
- 2 comments
#1373 - fix intervals file
Pull Request -
State: closed - Opened by FriederikeHanssen 9 months ago
- 1 comment
#1372 - Add test profile for ncbench
Pull Request -
State: closed - Opened by FriederikeHanssen 9 months ago
- 2 comments
#1371 - Not valid SNP_GRCh38_hg38_wChr.bed on GATK.GRCh38
Issue -
State: open - Opened by jbague 9 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 9 months ago
- 2 comments
Labels: bug
#1369 - Mutect2 error with Sarek 3.4.0
Issue -
State: open - Opened by mimifp 9 months ago
- 4 comments
Labels: bug
#1368 - Sambamba
Pull Request -
State: open - Opened by stavgrossfeld 9 months ago
- 2 comments
#1367 - sambamba/markdup
Issue -
State: open - Opened by stavgrossfeld 9 months ago
- 1 comment
Labels: enhancement
#1366 - NGSCHECKMATE_NCM
Issue -
State: open - Opened by LuciaNhuNguyen 9 months ago
- 6 comments
Labels: enhancement
#1365 - Template update for nf-core/tools version 2.11.1
Pull Request -
State: closed - Opened by mirpedrol 10 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 10 months ago
- 5 comments
#1363 - Minimum split_fastq value is 250
Issue -
State: closed - Opened by adamrtalbot 10 months ago
- 4 comments
Labels: bug
#1362 - Check docker.runOptions for spark
Issue -
State: open - Opened by maxulysse 10 months ago
#1361 - Increase run time
Issue -
State: closed - Opened by gitMakeCoffee 10 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 10 months ago
- 1 comment
#1359 - remove params from subworkflows
Pull Request -
State: closed - Opened by maxulysse 10 months ago
- 2 comments
#1358 - Replace DRAGMAP with NARFMAP
Pull Request -
State: open - Opened by edmundmiller 10 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 10 months ago
- 3 comments
Labels: bug
#1356 - ngscheckmate_bed is set incorrectly for GATK.GRCh37
Issue -
State: open - Opened by SPPearce 10 months ago
Labels: bug
#1355 - Allow to specify a local config file for snpEff
Issue -
State: open - Opened by maxulysse 10 months ago
Labels: enhancement
#1354 - Allow for snpEff db without versions
Issue -
State: open - Opened by maxulysse 10 months ago
Labels: enhancement
#1353 - use utils subworkflows
Pull Request -
State: open - Opened by maxulysse 10 months ago
- 1 comment
#1352 - Strelka malformed VCF header
Issue -
State: closed - Opened by gitMakeCoffee 10 months ago
- 3 comments
Labels: bug
#1351 - fix params in test profiles
Pull Request -
State: closed - Opened by maxulysse 10 months ago
- 2 comments
#1350 - update Dragmap
Pull Request -
State: closed - Opened by maxulysse 10 months ago
- 7 comments
#1349 - Fix nf-tests coming from nf-core/modules
Issue -
State: open - Opened by maxulysse 10 months ago
#1348 - Unpatch dragmap modules
Issue -
State: open - Opened by maxulysse 10 months ago
#1347 - Error while FASTP is running
Issue -
State: closed - Opened by cuppacuppa 10 months ago
- 6 comments
#1346 - No parameter for "penalty" in ASCAT segmentation
Issue -
State: open - Opened by MGCarta 10 months ago
- 1 comment
Labels: enhancement
#1345 - Preserve STDERR
Pull Request -
State: closed - Opened by sminot 10 months ago
- 2 comments
#1344 - enable qc when starting from VC
Pull Request -
State: closed - Opened by FriederikeHanssen 10 months ago
- 2 comments
#1343 - Paper review
Pull Request -
State: closed - Opened by FriederikeHanssen 10 months ago
- 1 comment
#1342 - VEP on Strelka indel output
Issue -
State: closed - Opened by frenkiboy 10 months ago
- 1 comment
Labels: question
#1341 - sarek on Kubernetes documentation
Issue -
State: closed - Opened by radaniba 10 months ago
- 1 comment
Labels: enhancement
#1340 - Add Azure megatests
Pull Request -
State: closed - Opened by adamrtalbot 10 months ago
- 19 comments
#1339 - Update sentieon-modules
Pull Request -
State: closed - Opened by asp8200 11 months ago
- 1 comment
#1338 - switch to using --write-index instead of samtools index
Pull Request -
State: open - Opened by FriederikeHanssen 11 months ago
- 3 comments
#1337 - Validate that only vcf.gz(.tbi) are provided
Issue -
State: open - Opened by FriederikeHanssen 11 months ago
Labels: enhancement, input validation
#1336 - Annotations for custom genome
Issue -
State: closed - Opened by rakesh-res 11 months ago
- 2 comments
Labels: question
#1335 - add docs for bcftools annotate params
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 6 comments
#1334 - remove extra v for slack report
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 1 comment
#1333 - Back to Dev
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 2 comments
#1332 - Java applications request too much memory
Issue -
State: open - Opened by rrlove-cdc 11 months ago
Labels: bug
#1331 - Add nf-test scatter CI testing
Issue -
State: open - Opened by Emiller88 11 months ago
Labels: testing
#1330 - Add SnpEff to full sized tests
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 1 comment
#1329 - haplotypecaller output unusual behavior without dbsnps/known-sites
Issue -
State: open - Opened by AJTDaedalus 11 months ago
Labels: bug
#1328 - Fix links to docs
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 1 comment
#1327 - Update all modules to have environment name
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 6 comments
#1326 - Misleading info in error message concerning invalid path to VEP-cache
Issue -
State: open - Opened by asp8200 11 months ago
- 3 comments
Labels: bug
#1325 - Update config files and other minor code polishing
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 6 comments
#1324 - Address code reviews from #1320
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 1 comment
#1323 - Error with ASCAT
Issue -
State: open - Opened by TuongViDang 11 months ago
- 3 comments
Labels: bug
#1322 - How to output allele-specific copy number in CNVkit?
Issue -
State: open - Opened by TuongViDang 11 months ago
Labels: enhancement
#1321 - ACTUAL Release 3.4
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 4 comments
#1320 - [DON' MERGE] Release 3.4.0
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 6 comments
#1319 - Bump version, set release names
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 1 comment
#1318 - fix issues with params json dump
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 3 comments
#1317 - update subway map
Pull Request -
State: closed - Opened by FriederikeHanssen 11 months ago
- 1 comment
#1316 - Fix UMI-link
Issue -
State: open - Opened by asp8200 11 months ago
Labels: bug
#1315 - Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows
Pull Request -
State: closed - Opened by asp8200 11 months ago
- 2 comments
#1314 - When both sentieon_haplotype and haplotypecaller are provided, config scopes are clashing
Issue -
State: closed - Opened by FriederikeHanssen 11 months ago
- 3 comments
Labels: bug
#1313 - Sarek stops after alignment and does not perform variant calling
Issue -
State: closed - Opened by sci-kai 11 months ago
- 16 comments
Labels: bug
#1312 - implementation of goleft/indexcov
Pull Request -
State: open - Opened by lindenb 11 months ago
- 3 comments
#1311 - update local modules
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 1 comment
#1309 - try better empty channel management for germline ressource in mutect2 subworkflow
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 2 comments
#1308 - Be consistent with the meta map for the reference files
Issue -
State: open - Opened by maxulysse 11 months ago
#1306 - Strelka requires `.crai` files to match format `PREFIX.cram.crai`
Issue -
State: open - Opened by awgymer 11 months ago
Labels: bug, input validation
#1304 - CHORES: update all modules
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 4 comments
#1303 - FEAT: Proper usage of vep_version
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 2 comments
#1302 - Fixing versions of nf-plugins
Pull Request -
State: closed - Opened by asp8200 11 months ago
- 4 comments
#1301 - FIX: nf-prov usage
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 4 comments
#1300 - Fix the version of the plugins used in Sarek
Issue -
State: closed - Opened by asp8200 11 months ago
Labels: enhancement
#1299 - Config setting `prov.formats`
Issue -
State: closed - Opened by LuciaNhuNguyen 11 months ago
- 12 comments
Labels: bug
#1298 - FIX: Remove use_annotation_cache_keys params
Pull Request -
State: closed - Opened by maxulysse 11 months ago
- 5 comments
#1297 - Sarek --download_cache does not work properly
Issue -
State: closed - Opened by Hadi90Eidgah 11 months ago
- 5 comments
Labels: bug
#1296 - ContaminationAssessment in the Sentieon-subworkflows TNseq and TNscope?
Issue -
State: open - Opened by asp8200 12 months ago
Labels: enhancement
#1295 - Sarek stops and cannot connect to amazonaws
Issue -
State: open - Opened by vmelichar 12 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 12 months ago
- 3 comments
#1293 - Samplesheets with more normal-samples per patient pass nf-validation
Issue -
State: open - Opened by asp8200 12 months ago
Labels: bug, input validation
#1292 - CNVKIT - Export cns file into seg format for IGV
Issue -
State: open - Opened by maxulysse 12 months ago
#1291 - Fix CODEOWNERS
Pull Request -
State: closed - Opened by Emiller88 12 months ago
- 1 comment
#1290 - minor nf test fixes
Pull Request -
State: closed - Opened by adamrtalbot 12 months ago
- 1 comment
#1289 - separate pytest from nftest
Pull Request -
State: closed - Opened by adamrtalbot 12 months ago
- 2 comments
#1288 - Add an nf-test CI
Pull Request -
State: closed - Opened by adamrtalbot 12 months ago
- 2 comments
#1287 - Adding labels to the local modules
Pull Request -
State: closed - Opened by asp8200 12 months ago
- 3 comments
#1286 - Created subworkflow for parsing samplesheet with nf-test
Pull Request -
State: closed - Opened by RaqManzano 12 months ago
- 5 comments
Labels: enhancement
#1285 - new subworkflow: samplesheet handling
Issue -
State: open - Opened by RaqManzano 12 months ago
- 1 comment
Labels: enhancement
#1284 - Switch to nf-core/fastq_create_umi_consensus_fgbio subworkflow
Pull Request -
State: closed - Opened by berguner 12 months ago
- 1 comment
#1283 - Usage.md: link to example samplesheet is broken
Issue -
State: open - Opened by FriederikeHanssen 12 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 12 months ago
- 3 comments
Labels: bug
#1281 - Readme uses bith light and dark logo at all times
Issue -
State: open - Opened by FriederikeHanssen 12 months ago
Labels: bug