Ecosyste.ms: Issues

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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

#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

#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

#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