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
Pass --rerun to GenerateReportForExperiment in SubmitExperimentReport…
Increase max SRA size to 100G
Revert "Add a priority to GenerateReportForExperiment"
Add a priority to GenerateReportForExperiment
Add perl to the dependencies for RSEM
Include webviewer templates in the package data
Generate a CWL workflow (WIP)
Add a check for validity of GEO metadata
Avoid overriding metadata in DownloadGeoSample and DownloadSraExperiment
Make SubmitExperimentReportToGemma rerunnable
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
Improve logic for detecting bulk RNA-Seq datasets
Addresses missing spots_with_mates column in SRA runinfo (
fix #93 )
Remove -f flag when calling fillBatchInfo
Bump min requirement for bioluigi to 0.3.4
Perform sample renaming for the MultiQC report
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
Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask
Relocate Gemma-specific configuration under [rnaseq_pipeline.gemma]
Make Gemma's appdata directory configurable
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
Few fixes for the webviewer
arteymixpushed 3 commits to master • 71c0247…533d237 • on Mar 20, 2024
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