Ecosyste.ms: Issues

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GitHub / genialis/resolwe-bio issues and pull requests

#1361 - Implement resolwe-bio process for fusion calling with Arriba

Pull Request - State: open - Opened by zkuralt 4 months ago

#1360 - Expose variant objects in python processes

Pull Request - State: open - Opened by gregorjerse 4 months ago

#1359 - Feature/private repo

Pull Request - State: open - Opened by gregorjerse 4 months ago

#1358 - Modify star.py and bbduk_star.py for fusion calling

Pull Request - State: closed - Opened by zkuralt 4 months ago

#1357 - Remove obsolete processes and scripts

Pull Request - State: closed - Opened by jkokosar 4 months ago

#1356 - Change iteration size in listener for kb models to 10000

Pull Request - State: closed - Opened by gregorjerse 4 months ago

#1355 - Add retries for SRA query in geo-import process

Pull Request - State: closed - Opened by jkokosar 4 months ago

#1353 - Use partial testing

Pull Request - State: closed - Opened by gregorjerse 5 months ago

#1352 - Add filters by sample to variant objects

Pull Request - State: open - Opened by gregorjerse 5 months ago

#1351 - Prepare release 58.0.0

Pull Request - State: closed - Opened by jkokosar 5 months ago

#1350 - Add changes to ``pca-beta`` process

Pull Request - State: closed - Opened by marcellevstek 5 months ago

#1349 - Fix coercing the number of threads to int

Pull Request - State: closed - Opened by romunov 5 months ago - 1 comment

#1346 - Implement peak calling in Cut & Run workflow

Pull Request - State: closed - Opened by jkokosar 5 months ago

#1345 - Prepare release 57.0.0

Pull Request - State: closed - Opened by jkokosar 5 months ago

#1342 - Fix debug must be set to true when building tests

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

#1341 - Bump dependencies

Pull Request - State: closed - Opened by gregorjerse 6 months ago

#1340 - Do not run type checks on every pull request

Pull Request - State: closed - Opened by gregorjerse 6 months ago

#1338 - Require Resolwe 40.x

Pull Request - State: closed - Opened by gregorjerse 6 months ago

#1336 - Add ``pca-beta`` process

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

#1335 - Prepare release 56.0.0

Pull Request - State: closed - Opened by jkokosar 7 months ago

#1333 - Add coverage configuration

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

#1332 - Build (pre)release automatically on tag push

Pull Request - State: closed - Opened by gregorjerse 7 months ago

#1331 - Prepare release 54.4.0

Pull Request - State: closed - Opened by jkokosar 8 months ago

#1330 - Use GRCh38.109 annotation database in snpEff

Pull Request - State: closed - Opened by jkokosar 8 months ago

#1329 - Upgrade PostgreSQL used in tests to version 16

Pull Request - State: closed - Opened by gregorjerse 8 months ago

#1328 - Rewrite Expression Aggregator process to Python

Pull Request - State: closed - Opened by jkokosar 8 months ago

#1327 - Remove entity descriptor fields

Pull Request - State: closed - Opened by gregorjerse 8 months ago

#1326 - Remove processes associated with 10x scRNA-seq

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

#1325 - Rename beta and remove legacy Cut&Run workflow

Pull Request - State: closed - Opened by romunov 8 months ago

#1324 - Prepare release 55.3.0

Pull Request - State: closed - Opened by jkokosar 8 months ago

#1323 - Fix handling of large files in ``samtools-depth`` process

Pull Request - State: closed - Opened by marcellevstek 8 months ago

#1322 - Remove RNA-SeQC from workflows and MultiQC

Pull Request - State: closed - Opened by marcellevstek 9 months ago

#1321 - Add gene body coverage information to MultiQC

Pull Request - State: closed - Opened by marcellevstek 9 months ago

#1320 - Add retry for reads prefetch in ``import-sra``

Pull Request - State: closed - Opened by marcellevstek 9 months ago

#1319 - Fix handling downsampled STAR inputs in MultiQC

Pull Request - State: closed - Opened by jkokosar 9 months ago

#1318 - Add support for Python 3.12, remove Jenkins configuration

Pull Request - State: closed - Opened by gregorjerse 9 months ago

#1317 - Feature/arc runners

Pull Request - State: closed - Opened by gregorjerse 9 months ago

#1316 - Add simple github actions workflow

Pull Request - State: closed - Opened by gregorjerse 9 months ago

#1315 - Migrate Jenkins workflow to Github Actions

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

#1314 - Fix MultiQC with MACS2 in broad peak mode

Pull Request - State: closed - Opened by jkokosar 9 months ago

#1313 - Prepare release 52.2.0

Pull Request - State: closed - Opened by jkokosar 9 months ago

#1312 - Add input option to exclude flags in ``samtools-bedcov``

Pull Request - State: closed - Opened by marcellevstek 10 months ago

#1311 - Add ``samtools-depth-single`` process

Pull Request - State: closed - Opened by marcellevstek 10 months ago

#1310 - Reword MACS2 documentation

Pull Request - State: closed - Opened by romunov 10 months ago

#1309 - Bump black version

Pull Request - State: closed - Opened by gregorjerse 10 months ago

#1308 - Fix input fields for ``workflow-cutnrun-beta``

Pull Request - State: closed - Opened by marcellevstek 11 months ago

#1307 - Feature: mutations

Pull Request - State: closed - Opened by gregorjerse 11 months ago

#1306 - Prepare release 55.1.0

Pull Request - State: closed - Opened by jkokosar 12 months ago

#1305 - Change the process type of ``samtools-bedcov``

Pull Request - State: closed - Opened by marcellevstek 12 months ago

#1304 - Change ``samtools-bedcov`` process

Pull Request - State: closed - Opened by marcellevstek 12 months ago - 2 comments

#1303 - Add Cut & Run preprocessing workflow

Pull Request - State: closed - Opened by marcellevstek 12 months ago

#1302 - Output normalized counts in DESeq2 process

Pull Request - State: closed - Opened by marcellevstek 12 months ago

#1301 - Fix ``qorts-qc`` hg19 annotation error

Pull Request - State: closed - Opened by marcellevstek 12 months ago

#1300 - Add Samtools bedcov as a process

Pull Request - State: closed - Opened by marcellevstek about 1 year ago

#1299 - Use downsampled alignment for RNA-SeQC in workflows

Pull Request - State: closed - Opened by marcellevstek about 1 year ago

#1298 - Prepare release 55.0.0

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

#1297 - Change RNA-SeQC data object label in workflows

Pull Request - State: closed - Opened by marcellevstek about 1 year ago

#1296 - Bump the version of resolwebio/common Docker image

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

#1295 - Prepare release 54.0.0

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

#1294 - Use Python 3.11 for tests

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

#1293 - Fix scaling in Cut & Run workflow

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

#1292 - Fix experimental model annotation in geo-import

Pull Request - State: closed - Opened by AnzeLovse about 1 year ago

#1291 - Add sample_annotation jinja expressions filter

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

#1290 - Update processes using annotations

Pull Request - State: closed - Opened by AnzeLovse about 1 year ago

#1289 - Modify workflows to include RNA-SeQC

Pull Request - State: closed - Opened by marcellevstek about 1 year ago

#1288 - Prepare release 53.2.0

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

#1287 - Report gene coverage and assigned reads

Pull Request - State: closed - Opened by marcellevstek about 1 year ago

#1286 - Prepare release 53.1.0

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

#1285 - Bump storage requirements in BWA processes

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

#1284 - Report assigned reads count by STAR quantification

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

#1282 - Prepare release 53.0.0

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

#1281 - Add mask option to VariantFiltration

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

#1280 - WIP: failing test

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

#1279 - Improve GEO import warnings for missing raw data

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

#1277 - Upgrade to Django 4.2

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

#1276 - Changed RNA-SeQC helper functions and tests

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

#1275 - Prepare release 52.1.0

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

#1274 - Set process resources in Bowtie aligners

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

#1273 - Fix SRA parameters to pass zero values in geo-import

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

#1272 - Add listener command to query Feature objects

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

#1271 - Prepare release 52.0.0

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

#1270 - Add RNA-SeQC and modify MultiQC process

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

#1269 - Always use Docker default seccomp profile

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

#1268 - Disable seccomp

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

#1267 - Fix BBDuk settings in RNA-seq VC workflow

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

#1266 - Require Resolwe 35.x

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

#1265 - Adjust process resource settings

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

#1264 - Prevent BBduk from stopping when lanes exceed cores

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

#1263 - Fix SRA import to accept 0 as minimum read length

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

#1262 - Support the use of BAM file as an input in the RNA-seq VC workflow

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