PavlidisLab rnaseq-pipeline issues

PavlidisLab / rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

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issues

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Use NCBI FTP server for downloading MINiML files

#95 arteymix opened 5 days ago
0
Handle SRA experiments with multiple lanes mapped on distinct runs

#94 arteymix opened 5 days ago
1
AttributeError: 'Series' object has no attribute 'spots_with_mates'

#93 arteymix closed 1 week ago
0
Duplicate row name 170942 when adding RNA-Seq data

#92 arteymix closed 2 months ago
1
Address already in use

#91 arteymix opened 3 months ago
2
Metadata in Prefetch tasks should use a GSM ID, not a SRX ID.

#90 arteymix opened 3 months ago
0
Reorganize high-level scripts into a rnaseq-pipeline-cli tool

#89 arteymix opened 8 months ago
0
Produce an error when fastq files are empty

#88 arteymix opened 8 months ago
0
Remove --clip and --skip-technical from fastq-dump

#87 arteymix opened 8 months ago
0
Include the webviewer tests on the CI

#86 arteymix opened 8 months ago
0
Report errors on the Slack channel

#85 arteymix opened 9 months ago
0
Use of uninitialized value $doesOpen in numeric eq (==) at contrib/RSEM/rsem-calculate-expression line 574

#84 arteymix opened 10 months ago
0
Add a homepage

#83 arteymix closed 9 months ago
0
RuntimeError: Unfulfilled dependency at run time: rnaseq_pipeline.tasks.SubmitExperimentBatchInfoToGemma

#82 arteymix closed 1 year ago
1
Add support for NextSeq 2000 (Mus musculus) (GPL30172)

#81 arteymix closed 1 year ago
1
Include environment variables from the Slurm jobs in the error logs

#80 arteymix closed 1 year ago
1
CI is stuck when setting up the Conda environment

#79 arteymix closed 4 months ago
0
Update MultiQC to 1.14

#78 arteymix closed 1 year ago
1
DeprecationWarning: Importing 'itsdangerous.json' is deprecated and will be removed in ItsDangerous 2.1. Use Python's 'json' modu le instead.

#77 arteymix closed 1 year ago
1
Unfulfilled dependency at runtime for SubmitExperimentBatchInfo

#76 arteymix opened 1 year ago
1
IndexError: single positional indexer is out-of-bounds while parsing runinfo file

#75 arteymix closed 1 year ago
1
Fix runinfo parsing with missing header

#74 arteymix closed 2 years ago
1
Fastas file ending with .fna are not detected when preparing RSEM/STAR indices

#73 arteymix closed 2 years ago
1
Evaluate cutadapt 4.0

#72 arteymix closed 1 year ago
1
Use Python 3.10 in CI

#71 arteymix closed 2 years ago
0
Reuse Bioluigi definitions for RSEM tasks

#70 arteymix opened 2 years ago
0
Update MultiQC to 1.11

#69 arteymix closed 2 years ago
0
Include the experiment ID and sample ID in Prefetch

#68 arteymix closed 4 months ago
1
Killed external tasks leave an empty error message

#67 arteymix opened 2 years ago
0
rnaseq_pipeline.sources.sra.DownloadSraExperimentRunInfo fails with exit status 255

#66 arteymix closed 9 months ago
1
Raise Error When SRX Only Has Empty Files

#65 Tu1026 closed 2 years ago
0
Batch information that has been deemed unuseable are not considered completed

#64 arteymix opened 2 years ago
0
Add a task to generate a summary of the tools, software and references used

#63 arteymix opened 2 years ago
0
Use luigi.TaskParameter for platforms and sources-specific tasks

#62 arteymix opened 2 years ago
0
Setup CI with GitHub Actions

#61 arteymix closed 2 years ago
1
Read with 3 parts break cutadapt with unexpected suffixes in the read ids

#60 arteymix closed 2 years ago
3
Trimmed FASTQs are not deleted when data is successfully submitted to Gemma

#59 arteymix opened 2 years ago
0
Build and install the shared memory cleanup tool during initial setup

#58 arteymix opened 3 years ago
0
Update MultiQC to 1.10

#57 arteymix closed 3 years ago
2
Batch information for split experiments

#56 sanjarogic opened 3 years ago
0
DownloadSraExperimentRunInfo should fail on an empty runinfo table

#55 arteymix closed 9 months ago
1
Adjust FastQC limits to be suitable for RNA-Seq

#54 arteymix opened 3 years ago
0
Add BGI-SEQ adapters to the FastQC report

#53 arteymix opened 3 years ago
0
Add support for Ion Torrent Proton platform

#52 arteymix opened 3 years ago
0
Add automated quality control checks before submitting data to Gemma

#51 arteymix opened 3 years ago
0
Add a timeout after submitting data to Gemma to account for caching

#50 arteymix closed 3 years ago
1
Adapt the Web viewer for other data sources

#49 arteymix opened 3 years ago
0
Migrate to Luigi 3.0.0

#48 arteymix closed 3 years ago
0
Add cutadapt section to MultiQC report

#47 arteymix opened 3 years ago
1
Only consider the relevant subset of samples when assessing batch info

#46 arteymix opened 4 years ago
0