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
#1280 - Updating link to sentieonDNAscopeModel file
Pull Request -
State: closed - Opened by asp8200 12 months ago
- 1 comment
#1279 - Parameter validation doesn't catch of unzipped vcf is supplied
Issue -
State: open - Opened by FriederikeHanssen 12 months ago
Labels: bug
#1278 - Update docs
Pull Request -
State: closed - Opened by FriederikeHanssen 12 months ago
- 1 comment
#1277 - Fix null value for joint calling with Mutect2
Pull Request -
State: closed - Opened by FriederikeHanssen 12 months ago
- 4 comments
#1276 - lane should be optional if unique
Issue -
State: open - Opened by maxulysse 12 months ago
Labels: enhancement
#1275 - Merge and normalise VCF files
Issue -
State: open - Opened by Matteodigg 12 months ago
Labels: enhancement
#1274 - null value in mutect2 subworkflow
Issue -
State: closed - Opened by maxulysse 12 months ago
- 7 comments
Labels: bug
#1273 - Missing bam files
Issue -
State: open - Opened by maxulysse 12 months ago
- 4 comments
Labels: bug
#1272 - Ncbench
Pull Request -
State: closed - Opened by FriederikeHanssen 12 months ago
- 7 comments
#1271 - CHORES: Back to dev
Pull Request -
State: closed - Opened by maxulysse 12 months ago
- 1 comment
#1270 - FIX: revert controlfreec-assesssignificance
Pull Request -
State: closed - Opened by maxulysse 12 months ago
- 1 comment
#1269 - Receiving new error (ERROR ~ Unexpected error [EOFException])
Issue -
State: open - Opened by sxv 12 months ago
- 2 comments
Labels: bug
#1268 - EnsemblVEP output only contains HTML report
Issue -
State: closed - Opened by slives-lab almost 1 year ago
- 2 comments
Labels: bug
#1267 - Add bcftools annotate
Pull Request -
State: closed - Opened by grantn5 almost 1 year ago
- 3 comments
Labels: Ready for Review
#1266 - Ncbench
Pull Request -
State: closed - Opened by FriederikeHanssen almost 1 year ago
- 1 comment
#1265 - AlphaMissense VEP Plugin Integration
Issue -
State: open - Opened by Moe94 about 1 year ago
Labels: enhancement
#1264 - FEAT: Release Canditate 3.3.2
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1263 - FEAT: RC 3.3.2
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 3 comments
#1262 - FEAT: prepare RC 3.3.2
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1261 - FEAT: add merge to cache checks
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1260 - The sample-sheet only contains tumor-samples
Issue -
State: open - Opened by bounlu about 1 year ago
- 28 comments
Labels: bug
#1259 - Add nf-prov
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 6 comments
#1258 - fastqc docker image updated to last stable version (previous one was …
Pull Request -
State: closed - Opened by gitanoqevaporelmundoentero about 1 year ago
- 4 comments
#1257 - SNPEFF annotation process interrupted when no cache available
Issue -
State: closed - Opened by ducminhnguyenle about 1 year ago
- 3 comments
Labels: bug
#1256 - FIX: remove spaces in controlfreec modules
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1255 - flowcellLaneFromFastq cannot handle weird fastq header
Issue -
State: open - Opened by brucemoran about 1 year ago
- 4 comments
Labels: bug
#1254 - Important! Template update for nf-core/tools v2.10
Pull Request -
State: closed - Opened by nf-core-bot about 1 year ago
- 1 comment
#1253 - Error out when user provides both custom genome files (fasta, fai, dict, etc) in addition to --genome param
Issue -
State: open - Opened by robsyme about 1 year ago
- 1 comment
Labels: enhancement
#1252 - [DRAFT] Add NGSCheckMate in as part of a cram sampleQC subworkflow
Pull Request -
State: closed - Opened by SPPearce about 1 year ago
- 10 comments
#1251 - Output files for CNVkit incorrect
Issue -
State: open - Opened by parth2608 about 1 year ago
- 12 comments
Labels: bug
#1250 - Stop ignoring parameter validation, lenient mode is sufficient
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
#1249 - Add Azure megatests
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
- 1 comment
Labels: enhancement
#1248 - FEAT: Improve documentation for annotation cache
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1247 - fix result path
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1246 - back to dev
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1245 - prepare release
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1244 - Candidate release 3.3.1
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1243 - FEAT: Improve schema usage for input
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1242 - Simplify sentieon test license server usage
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1241 - Update controlfreec version
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 3 comments
#1240 - FIX: Disable JVM hotspot in gatk4 modules
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 2 comments
#1239 - `ASSESS_SIGNIFICANCE` fails with Rscript error
Issue -
State: open - Opened by bounlu about 1 year ago
- 9 comments
Labels: bug
#1238 - Introducing profile sentieon_test_licence
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 6 comments
#1237 - Remove Sentieon license details from -profile test
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 7 comments
#1236 - FIX: remove check annotation folders existence when no annotation
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1235 - Running out of disk space
Issue -
State: closed - Opened by sxv about 1 year ago
- 3 comments
Labels: question
#1234 - Add gene annotation on cnvkit for WGS (--annotate)
Issue -
State: open - Opened by migmarbor about 1 year ago
Labels: enhancement
#1233 - Question regarding sarek dockers :
Issue -
State: open - Opened by ChitrArpita about 1 year ago
- 13 comments
#1232 - Fix Zenodo ID in manifest
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1231 - Back to dev
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 2 comments
#1230 - update checksums due to input csv changes
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1229 - FIX: gatk4_spark checksum
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1228 - CI tests for spark are not passing
Issue -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
Labels: bug
#1227 - FIX: update modules
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1226 - Error when write a file running Mutect2 with Sarek
Issue -
State: open - Opened by mimifp about 1 year ago
- 7 comments
Labels: bug
#1225 - FIX: Better coverage for all tests
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 3 comments
#1224 - New version of BCFTOOLS_SORT-module with '--temp-dir .' added as opti…
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 3 comments
#1223 - Add cnvkit genemetrics
Pull Request -
State: closed - Opened by grantn5 about 1 year ago
- 11 comments
#1222 - Update documentation around VEP and snpEff cache
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 2 comments
#1221 - remove lane after tracking in id to ensure proper merging after mapping
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 4 comments
#1220 - Joint calling: Fix meta map info for proper joining
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 6 comments
#1219 - Revert md5sums for some csvs from the mutec2_manual test
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 3 comments
#1218 - FIX: Remove singularity tests from GHA
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1217 - FIX: Final fix for joint_mutect2 tumor_only in mutect2 subworkflow
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1216 - FIX: Better coverage in _all variant calling subworkflows
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1215 - FIX: fix mutect2 meta id issue in tumor_only workflow
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 8 comments
#1214 - Don't pass in intervals file to freec
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 3 comments
#1213 - GATK time limit excedded error
Issue -
State: closed - Opened by frenkiboy about 1 year ago
- 1 comment
Labels: bug
#1212 - Use matrix for all aws tests GHA
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 4 comments
#1211 - Use matrix for awstest github action
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 2 comments
#1210 - Replace param haplotypecaller_filter, haplotyper_filter and dnascope_filter with variant_filter
Issue -
State: closed - Opened by asp8200 about 1 year ago
- 2 comments
Labels: enhancement
#1209 - Add a parameter corresponding to -canonList <file> option of snpEff ann
Issue -
State: open - Opened by YeHW about 1 year ago
- 1 comment
Labels: enhancement
#1208 - Add --annotate flag to CNVKIT_BATCH
Issue -
State: open - Opened by SpikyClip about 1 year ago
Labels: enhancement
#1207 - `snpeff_cache` folder is empty
Issue -
State: open - Opened by bounlu about 1 year ago
- 10 comments
Labels: bug
#1206 - `WARN`: Uninitialized parameters
Issue -
State: closed - Opened by bounlu about 1 year ago
- 1 comment
Labels: bug
#1205 - remove push: dev CI trigger
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 2 comments
#1204 - FIX: nf-validation schema_input
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1203 - FIX: Singularity error on test profiles
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1202 - ci: Remove Nextflow caching
Pull Request -
State: closed - Opened by Emiller88 about 1 year ago
- 6 comments
Labels: testing
#1201 - Reduce hitting Github API rate limits to prevent throttling
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 2 comments
#1200 - Overhaul GHA
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 17 comments
#1199 - Candidate release 3.3.0
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1198 - CHORES: Prepare 3.3
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1197 - Greatly improve tower.yml file
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 1 comment
#1196 - More sensible default for use_annotation_cache_keys
Pull Request -
State: closed - Opened by maxulysse about 1 year ago
- 3 comments
#1195 - Access Denied (Service: Amazon S3; ...)
Issue -
State: closed - Opened by davetang about 1 year ago
- 13 comments
Labels: bug
#1194 - Start pipeline from intermediate cram files
Issue -
State: closed - Opened by sxv about 1 year ago
- 5 comments
Labels: bug
#1193 - Dnascope module and subworkflow in Sarek
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 11 comments
#1192 - added missing output documentation for ASCATprofile.png
Pull Request -
State: closed - Opened by JohannesKersting about 1 year ago
- 2 comments
#1191 - Missing output documentation for ascat ASCATprofile plot
Issue -
State: closed - Opened by JohannesKersting about 1 year ago
- 1 comment
Labels: docs
#1190 - Add a tower.yml and populate it with the expected output from sarek
Issue -
State: closed - Opened by maxulysse about 1 year ago
Labels: enhancement
#1189 - Update awsfulltest to use action v2
Pull Request -
State: closed - Opened by adamrtalbot about 1 year ago
- 7 comments
#1188 - [WIP] --tools is now case insensitive
Pull Request -
State: open - Opened by adamrtalbot about 1 year ago
- 11 comments
#1187 - Improvement: make --tools case insensitive
Issue -
State: open - Opened by adamrtalbot about 1 year ago
- 1 comment
Labels: enhancement
#1186 - Annote unfiltered mutect reads if no filtering is done
Issue -
State: open - Opened by FriederikeHanssen about 1 year ago
Labels: enhancement
#1185 - sarek failed at BQSR
Issue -
State: closed - Opened by ChitrArpita about 1 year ago
- 2 comments
#1184 - Extending tests for sentieon joint germline AND avoiding duplicated variants in VQSR vcfs
Pull Request -
State: closed - Opened by asp8200 about 1 year ago
- 2 comments
#1183 - Update docs
Pull Request -
State: closed - Opened by FriederikeHanssen about 1 year ago
- 1 comment
#1182 - Managing CRAM compression level
Issue -
State: open - Opened by dr-yoon about 1 year ago
- 3 comments
Labels: enhancement
#1181 - Fix join mismatch error for joint tumor only Mutect2
Pull Request -
State: closed - Opened by berguner about 1 year ago
- 1 comment