rnaseq

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This should be possible via the suggested implementation in [this issue](https://github.com/CGATOxford/UMI-tools/issues/465). The flow will be very similar to what we are doing with STAR/Salmon.

drpatelh

### Description of the bug Hi, I get get the following error message when running nf-core/rnaseq test. And comments/suggestions?  ### Command used and terminal output ```console $ nextflow run...

dalinlee

### Description of feature [Homepage](https://github.com/OceanGenomics/mudskipper) [Bioconda](https://bioconda.github.io/recipes/mudskipper/README.html?highlight=mudskipper#package-package%20'mudskipper') Currently, we don't have a native quantification method for HISAT2 genomic alignments because we need to project these onto transcriptomic alignments for accurate quantification...

drpatelh

### Description of feature Dear nfcore/rnaseq team, I have encountered a recurring issue with `save_merged_fastq`. I would like a directory that contains a single fastq for each sample in the...

ojziff

Unclear description of output files for alignment and quantification step

4

## Request for unambiguous description of the most important output files First, apologies and feel free to close this issue if this has been addressed in `nf-core/rnaseq/3.4`. When running `nf-core/rnaseq/3.0`,...

danwiththeplan

star_rsem aligner fails if started from NFS

1

### Description of the bug When nextflow is started from an NFS mount (AWS EFS volume), the `star_rsem` aligner fails at the ` rsem-calculate-expression` step. It appears that this step...

schaffman5

SALMON_TX2GENE failing when skip_alignment is true and pseudo_aligner is salmon

9

## Check Documentation I have checked the following places for your error: - [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [X] [nf-core/rnaseq pipeline documentation](https://nf-co.re/rnaseq/usage) ## Description of the bug When using the...

JSchoenbachler

DESEQ2 using more cores (29) than requested (6)

2

### Description of the bug We encountered this issue running the pipeline on our Slurm cluster. They have rather strict policies in place that result in jobs being automatically terminated...

jambler24

add optional argument to let infer_experiment.py decide strandedness

6

Dear nfcore/rnaseq team, The fetchngs > rnaseq pipline is simply awesome! Because sample **strandedness** is almost never documented in GEO or ENA metadata, one thing that could be improved is...

ojziff

genome requirement with --pseudo_aligner salmon and --skip_alignment

5

## Check Documentation I have checked the following places for your error: I have checked both of these and looked through the introduction to see which steps might require the...

didillysquat