genialis/resolwe-bio issues and pull requests

#1261 - Prepare release 51.0.0

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

#1260 - Add output field feature_type to STAR quantification process

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

#1259 - Optimize resource usage for interactive processes

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

#1258 - Add option for 2-pass mode to BBDuk-STAR workflow

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

#1257 - Support filtering by genotype fields in process Mutations table

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

#1256 - Add an option to filter by genotype fields in GATK VariantFiltration

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

#1255 - Deprecate old STAR processes

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

#1254 - Prepare release 50.0.0

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

#1253 - Add cDNA index to QoRTs inputs in STAR-based RNA-seq workflow

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

#1252 - Require resolwe 33.x

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

#1251 - Fix/feature ordering

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

#1250 - Update readthedocs config

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

#1249 - Add STAR-based RNA-seq workflow

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

#1248 - Bump Python version to 3.10 in readthedocs config

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

#1247 - Add process STAR gene quantification

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

#1246 - Use Python 3.10 for tests on Jenkins

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

#1245 - Add processes STAR and STAR genome index with 2.7.10b STAR version

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1244 - Add option to compute gene counts in STAR

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1243 - Prepare release 49.0.0

Pull Request - State: closed - Opened by jkokosar almost 2 years ago

#1242 - Fix depth calculation by pysam in Mutations table process

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1241 - Extend RNA-seq variant calling workflow

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1240 - Update process categories and remove "Show advanced options" checkbox

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1239 - Add memory limit to RNA-seq variant calling preprocess

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago - 1 comment

#1238 - Replace old RNA-seq workflow with beta

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1237 - Add mutation_status fields to general sample descriptor schema

Pull Request - State: closed - Opened by jkokosar almost 2 years ago

#1236 - Add process SnpEff for single-sample

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1235 - Add option for interval padding to GATK HaplotypeCaller

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1234 - Remove comparison to reference in process Mutations table

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1233 - Fix per-lane rc output in featureCounts beta and featureCounts prepararation for MultiQC

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1232 - Fix the check for genome builds of inputs in process snpEff

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1231 - Remove group nesting for QC fields in General descriptor schema

Pull Request - State: closed - Opened by OtonicarJan almost 2 years ago

#1230 - WIP Grgeor: Change processes of the General RNA-seq pipeline to support per-lane QC

Pull Request - State: closed - Opened by gregorjerse almost 2 years ago

#1229 - Enable ordering on knowledge-base endpoints

Pull Request - State: closed - Opened by dblenkus about 2 years ago - 1 comment

#1228 - Prepare release 48.0.0

Pull Request - State: closed - Opened by gregorjerse about 2 years ago

#1227 - Fix hidden fields in Samtools view process

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago - 1 comment

#1226 - Prepare release 47.4.0

Pull Request - State: closed - Opened by jkokosar about 2 years ago - 1 comment

#1225 - Change label values of the field biomarkers_pdl1_tps_cat in General descriptor schema

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1224 - Change processes of the General RNA-seq pipeline to support per-lane QC

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1223 - Feature/redis connection string

Pull Request - State: closed - Opened by gregorjerse about 2 years ago

#1222 - Add processes Samtools view and Samtools coverage

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago - 2 comments

#1221 - Output all detected input variants in Mutations table process

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1220 - Change separators in field names in General descriptor schema

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1219 - Rename group general_information to general in general DS

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1218 - Prepare release 47.3.0

Pull Request - State: closed - Opened by jkokosar about 2 years ago

#1217 - Support GEO series with EBI samples in GEO import

Pull Request - State: closed - Opened by AnzeLovse about 2 years ago

#1216 - Symlink individual Salmon outputs in the MultiQC process

Pull Request - State: closed - Opened by AnzeLovse about 2 years ago

#1215 - Bump version of RNA-seq VC preprocess

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1214 - Fix sample naming in the MultiQC report

Pull Request - State: closed - Opened by AnzeLovse about 2 years ago

#1213 - Flatten General descriptor schema

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago - 1 comment

#1212 - Prepare release 47.2.0

Pull Request - State: closed - Opened by jkokosar about 2 years ago

#1211 - Revert RNA-seq VC workflow to previous version

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1210 - Bump memory requirements for RNA-seq variant calling preprocess

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1209 - Support geneset as input to process Mutations table

Pull Request - State: closed - Opened by OtonicarJan about 2 years ago

#1208 - Add dicty-time-series descriptor schema

Pull Request - State: closed - Opened by jkokosar about 2 years ago

#1207 - Prepare release 47.1.0

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1206 - Add options to calculate variance of counts in Salmon RNA-seq workflow

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1205 - Add process RNA-seq variant calling preprocess

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1204 - Add optional calculation of variance in abundance estimates in Salmon Quant

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago - 2 comments

#1203 - Prepare release 47.0.0

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1202 - Require Resolwe 31.x

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1201 - Feature/faster test

Pull Request - State: closed - Opened by gregorjerse over 2 years ago

#1200 - Fixes for the ChIP-seq pipeline

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1199 - Prepare release 46.0.0

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1198 - Bump memory requirements in xengsort-index

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1197 - Generalize bigWig calculation

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1196 - Remove make_report.py from resolwe-bio

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1195 - Fix fragment length and memory issues in macs2-callpeak

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1194 - Use resolwebio/methylation_arrays:1.1.0 in methylation-array-sesame

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1193 - Use resolwebio/chipseq:6.1.0 in chipqc process

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1192 - Fix variants_filtered output in Variant filtering (CheMut)

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1191 - Update merge FASTQ process type

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1190 - Fix sporadically failing macs2 tests

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1189 - Add xengsort processes

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1188 - Add unified descriptor schema

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago - 1 comment

#1187 - Prepare release 45.0.0

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1186 - Remove BigWig outputs created with bamtobigwig.sh

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1185 - Update images in WGBS and ChIP-seq processes

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1184 - Add GATK SelectVariants to process Variant filtering (CheMut)

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1183 - Remove Docker files from project

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1182 - Handle empty input VCF files in Mutations table process

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1181 - Deprecate slamdunk

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1180 - Update data naming

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1179 - Use resolwebio/common Docker image for metadata upload

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1178 - Add openpyxl to resolwebio/common Docker image

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago - 1 comment

#1177 - Prepare release 44.1.0

Pull Request - State: closed - Opened by jkokosar over 2 years ago

#1176 - Fix handling missing relations in merge-sample processes

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1175 - Small fixes for reference-space and upload-ml-expression processes

Pull Request - State: closed - Opened by JureZmrzlikar over 2 years ago

#1174 - Replace the bash version of macs2-callpeak process

Pull Request - State: closed - Opened by AnzeLovse over 2 years ago

#1173 - Add check for presence of reference variants in process Mutations table

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1172 - Update GATK in CheMut processes to GATK4

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#1167 - Fix input schema in pipeline RNA-seq Variant Calling

Pull Request - State: closed - Opened by OtonicarJan over 2 years ago

#763 - Support automatic releasing to PyPI

Pull Request - State: closed - Opened by dblenkus over 5 years ago - 3 comments

GitHub / genialis/resolwe-bio issues and pull requests