Comments (3)
We should extract the batch information from each FASTQs in a separate task so that we can get rid of the whole file earlier.
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It would also be nice to isolate this work within the SRA source.
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This is now performed in SubmitExperimentToGemma
which ensures that data and batch information have been successfully submitted first.
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Related Issues (20)
- IndexError: single positional indexer is out-of-bounds while parsing runinfo file HOT 1
- Unfulfilled dependency at runtime for SubmitExperimentBatchInfo HOT 1
- DeprecationWarning: Importing 'itsdangerous.json' is deprecated and will be removed in ItsDangerous 2.1. Use Python's 'json' modu le instead. HOT 1
- Update MultiQC to 1.14 HOT 1
- CI is stuck when setting up the Conda environment
- Include environment variables from the Slurm jobs in the error logs HOT 1
- Add support for NextSeq 2000 (Mus musculus) (GPL30172) HOT 1
- RuntimeError: Unfulfilled dependency at run time: rnaseq_pipeline.tasks.SubmitExperimentBatchInfoToGemma HOT 1
- Use of uninitialized value $doesOpen in numeric eq (==) at contrib/RSEM/rsem-calculate-expression line 574
- Report errors on the Slack channel
- Include the webviewer tests on the CI
- Remove --clip and --skip-technical from fastq-dump
- Produce an error when fastq files are empty
- Reorganize high-level scripts into a rnaseq-pipeline-cli tool
- Metadata in Prefetch tasks should use a GSM ID, not a SRX ID. HOT 1
- Address already in use HOT 2
- Duplicate row name 170942 when adding RNA-Seq data HOT 1
- AttributeError: 'Series' object has no attribute 'spots_with_mates'
- Handle SRA experiments with multiple lanes mapped on distinct runs HOT 1
- Use NCBI FTP server for downloading MINiML files HOT 1
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