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Fix bug when setting is_paired

arteymixpushed 3 commits to master • 0de706c…1e1cce2 • 
on Nov 29, 2024

Add --force-single-end and --force-paired-reads

arteymixpushed 1 commit to master • 8e71bc4…0de706c • 
on Oct 28, 2024

Pass --rerun to GenerateReportForExperiment in SubmitExperimentReport…

arteymixpushed 1 commit to master • 67570e9…8e71bc4 • 
on Sep 3, 2024

Increase max SRA size to 100G

arteymixpushed 2 commits to master • eeae8be…67570e9 • 
on Sep 3, 2024

Revert "Add a priority to GenerateReportForExperiment"

arteymixpushed 1 commit to master • ebde490…eeae8be • 
on Aug 30, 2024

Add a priority to GenerateReportForExperiment

arteymixpushed 1 commit to master • 298d201…ebde490 • 
on Aug 30, 2024

Add perl to the dependencies for RSEM

arteymixpushed 1 commit to master • dddefee…298d201 • 
on Aug 26, 2024

Include webviewer templates in the package data

arteymixpushed 1 commit to master • ddafd0c…dddefee • 
on Aug 23, 2024

variable name update

arteymixcreated features/fastqdump_splitting • 2daeb3d • 
on Aug 19, 2024

Generate a CWL workflow (WIP)

arteymixcreated wip/cwl • 8123bc4 • 
on Aug 19, 2024

Add a Makefile

arteymixpushed 1 commit to master • 632542d…ddafd0c • 
on Aug 19, 2024

Use Python 3.9 on the CI

arteymixpushed 1 commit to master • bbaf421…632542d • 
on Aug 19, 2024

Add a check for validity of GEO metadata

arteymixpushed 1 commit to master • 16f249d…bbaf421 • 
on Aug 19, 2024

Avoid overriding metadata in DownloadGeoSample and DownloadSraExperiment

arteymixpushed 1 commit to master • ae02f56…16f249d • 
on Aug 13, 2024

Make SubmitExperimentReportToGemma rerunnable

arteymixpushed 1 commit to master • fed06f5…ae02f56 • 
on Aug 13, 2024

Drop the paired_read_expeirments option and simplify pairedness check

arteymixpushed 2 commits to master • 7ba68a1…fed06f5 • 
on Aug 13, 2024

Add a 2 hours walltime limit for prefetch tasks

arteymixpushed 1 commit to master • 1a660ed…7ba68a1 • 
on Aug 13, 2024

Improve logic for detecting bulk RNA-Seq datasets

arteymixpushed 1 commit to master • b626a41…1a660ed • 
on Jul 3, 2024

Addresses missing spots_with_mates column in SRA runinfo (fix #93)

arteymixpushed 1 commit to master • 51d5874…b626a41 • 
on Jun 25, 2024

Remove -f flag when calling fillBatchInfo

arteymixpushed 1 commit to master • a34826a…51d5874 • 
on Jun 14, 2024

Bump min requirement for bioluigi to 0.3.4

arteymixpushed 1 commit to master • 56984af…a34826a • 
on Jun 7, 2024

Perform sample renaming for the MultiQC report

arteymixpushed 1 commit to master • fb399fa…56984af • 
on Jun 7, 2024

Add a systemd unit for running the pipeline and use conda run

arteymixpushed 2 commits to master • 4352fec…fb399fa • 
on May 23, 2024

Add ssRNA-seq to the list of supported strategies

arteymixpushed 1 commit to master • cdbe165…4352fec • 
on May 21, 2024

Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask

arteymixpushed 1 commit to master • ab6b567…cdbe165 • 
on May 21, 2024

Relocate Gemma-specific configuration under [rnaseq_pipeline.gemma]

arteymixpushed 1 commit to master • ac1da2a…ab6b567 • 
on May 21, 2024

Make Gemma's appdata directory configurable

arteymixpushed 1 commit to master • acf0e84…ac1da2a • 
on May 21, 2024

Remove unused STAR_CLEANUP_SCRIPT config

arteymixpushed 2 commits to master • 31f8199…acf0e84 • 
on May 17, 2024

Add a script for synchronizing the MultiQC reports

arteymixpushed 3 commits to master • 533d237…31f8199 • 
on May 9, 2024

Few fixes for the webviewer

arteymixpushed 3 commits to master • 71c0247…533d237 • 
on Mar 20, 2024