Issues

• Add a CLI tool to remove the outputs of a given experiment

  PavlidisLab/rnaseq-pipeline#112 · Filter by author arteymix opened on Feb 27, 2026
  1

• Port the CLI to click

  PavlidisLab/rnaseq-pipeline#111 · Filter by author arteymix opened on Feb 27, 2026

• Add --ignore-mate (or --layout override) to submit-experiment

  Feature

  PavlidisLab/rnaseq-pipeline#110 · Filter by author arteymix opened on Feb 26, 2026

• Include Cell Ranger web_summary.html in the Web viewer

  Feature

  PavlidisLab/rnaseq-pipeline#109 · Filter by author cyan864 opened on Feb 26, 2026
  1

• Delete the lockfile when a prefetch task fails

  PavlidisLab/rnaseq-pipeline#107 · Filter by author arteymix opened on Jan 7, 2026 · 2.2.0

• Make the MultiQC report depend on the cutdapts report, not the trimmed reads

  PavlidisLab/rnaseq-pipeline#106 · Filter by author arteymix opened on Oct 29, 2025
  1

• Group cutadapt and FastQC results in the MultiQC report

  PavlidisLab/rnaseq-pipeline#105 · Filter by author arteymix opened on Oct 26, 2025
  

• Have a fast mechanism for retrieving batch information from FASTQ files

  PavlidisLab/rnaseq-pipeline#104 · Filter by author arteymix opened on Oct 23, 2025

• CI fails because /rest/v2/datasets/GSE110256/hasbatch requires admin role

  PavlidisLab/rnaseq-pipeline#96 · Filter by author arteymix opened on Oct 28, 2024
  1

• Include the webviewer tests on the CI

  PavlidisLab/rnaseq-pipeline#86 · Filter by author arteymix opened on Oct 17, 2023

• Report errors on the Slack channel

  PavlidisLab/rnaseq-pipeline#85 · Filter by author arteymix opened on Sep 25, 2023

• Use of uninitialized value $doesOpen in numeric eq (==) at contrib/RSEM/rsem-calculate-expression line 574

  bug
  PavlidisLab/rnaseq-pipeline#84 · Filter by author arteymix opened on Aug 28, 2023

• Killed external tasks leave an empty error message

  PavlidisLab/rnaseq-pipeline#67 · Filter by author arteymix opened on Nov 10, 2021

• Use luigi.TaskParameter for platforms and sources-specific tasks

  enhancement
  PavlidisLab/rnaseq-pipeline#62 · Filter by author arteymix opened on Aug 16, 2021

• Build and install the shared memory cleanup tool during initial setup

  PavlidisLab/rnaseq-pipeline#58 · Filter by author arteymix opened on Jun 25, 2021
  1

• Batch information for split experiments

  PavlidisLab/rnaseq-pipeline#56 · Filter by author sanjarogic opened on Mar 8, 2021

• Adjust FastQC limits to be suitable for RNA-Seq

  PavlidisLab/rnaseq-pipeline#54 · Filter by author arteymix opened on Feb 1, 2021
  1

• Add BGI-SEQ adapters to the FastQC report

  PavlidisLab/rnaseq-pipeline#53 · Filter by author arteymix opened on Feb 1, 2021

• Add support for Ion Torrent Proton platform

  PavlidisLab/rnaseq-pipeline#52 · Filter by author arteymix opened on Jan 26, 2021

• Add automated quality control checks before submitting data to Gemma

  enhancement
  PavlidisLab/rnaseq-pipeline#51 · Filter by author arteymix opened on Jan 15, 2021
  

• Adapt the Web viewer for other data sources

  enhancement
  PavlidisLab/rnaseq-pipeline#49 · Filter by author arteymix opened on Sep 7, 2020

• RSEM temporary file cleanup does not always work

  bug
  PavlidisLab/rnaseq-pipeline#39 · Filter by author arteymix opened on Feb 27, 2020 · 2.2.0
  1

• Make it less disruptive to queue new experiments

  enhancement
  PavlidisLab/rnaseq-pipeline#30 · Filter by author arteymix opened on Jan 10, 2020
  1

• Let sources handle taxons and other metadata

  enhancement
  PavlidisLab/rnaseq-pipeline#29 · Filter by author arteymix opened on Jan 9, 2020

• Use fasterq-dump

  enhancement
  PavlidisLab/rnaseq-pipeline#22 · Filter by author arteymix opened on Nov 15, 2019