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

Status: Open.

#112 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Feb 27, 2026

Port the CLI to click

Status: Open.

#111 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Feb 27, 2026

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

Status: Open.

Feature

#110 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Feb 26, 2026

Include Cell Ranger web_summary.html in the Web viewer

Status: Open.

Feature

#109 In PavlidisLab/rnaseq-pipeline;

· cyan864 opened on Feb 26, 2026

Delete the lockfile when a prefetch task fails

Status: Open.

#107 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Jan 7, 2026

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2.2.0

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

Status: Open.

#106 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Oct 29, 2025

Group cutadapt and FastQC results in the MultiQC report

Status: Open.

#105 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Oct 26, 2025

Have a fast mechanism for retrieving batch information from FASTQ files

Status: Open.

#104 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Oct 23, 2025

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

Status: Open.

#96 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Oct 28, 2024

Include the webviewer tests on the CI

Status: Open.

#86 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Oct 17, 2023

Report errors on the Slack channel

Status: Open.

#85 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Sep 25, 2023

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

bug

Status: Open.

#84 In PavlidisLab/rnaseq-pipeline;

· arteymix opened on Aug 28, 2023