rna-seq-kallisto-sleuth

rna-seq-kallisto-sleuth copied to clipboard

:robot: I have created a release *beep* *boop* --- ## [2.4.1](https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/compare/v2.4.0...v2.4.1) (2022-10-11) ### Bug Fixes * channel order for bioconductor package download ([f57044a](https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/commit/f57044a4a1a571fcf21ce7881b32f82a3fd09265)) * correct default value for representative_transcripts and...

github-actions[bot]

Before, giving a wrong value for that key has led to a very technical error deeply buried in some R script.

johanneskoester

InputFunctionException in line 29 .../quant.smk

1

The error message: ``` $ snakemake --cores 80 --use-conda --dry-run Building DAG of jobs... ~/miniconda3/envs/snakeflow-kallisto-sleuth/lib/python3.9/site-packages/pandas/core/indexing.py:925: PerformanceWarning: indexing past lexsort depth may impact performance. return self._getitem_tuple(key) InputFunctionException in line 29 of...

amitfenn

merge samples in kallisto_quant step

2

This PR implements sample merging by providing kallisto with all the units of a sample at once. I.e. if multiple sequencing runs are provided for a sample as units, kallisto...

dlaehnemann

Missing input files for rule kallisto_index:

1

Sorry if this is a dumb question. I'm very new to snakemake. I got the following error and I don't know how to fix it. MissingInputException in line 1 of...

trishorts

Checkpoints are not needed here anymore, because the report flag now can take a directory and add all contained files into the report, see [here](https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html). Hence, we need to replace...

johanneskoester

Check if we can get the curated SIGNOR database into a format that SPIA can use for its pathway enrichment analysis. It probably makes sense to start from this: https://signor.uniroma2.it/getPathwayData.php?relations

dlaehnemann

When an entry is added to or removed from `units.tsv`, this should prompt a rerun of the whole workflow, at least from rules `sleuth_init` and `compose_samplesheet` onward. This is currently...

HenningTimm

I wonder if you guys had plans to add annotation to the transcriptome?

1

Do you guys have any plans to add an annotation pipeline to the transcriptome (like through Trinotate). I am struggling with that portion of the analysis and really like the...

Buuntu

manuelphilip