Oliver Ziff

row_split reorders row_order even with cluster_row_slices = FALSE

9

Hi @jokergoo I am unable to control the heatmap ordering when using `row_split` and `row_order` even when specifying `cluster_row_slices = FALSE`. The row order is correct when I don't specify...

DESEQ2_QC_STAR_SALMON timeout with rlog and 400 samples

1

I ran rnaseq v3.8.1 on 400 samples. Failed as I got a timeout after 8hrs on `DESEQ2_QC_STAR_SALMON` process. It was still running `rlog` after 8 hours with the message: ```...

save_merged_fastq output directory to contain both fastqs that need merging and those that dont

1

### 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...

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...

### Description of feature Hi there, Many RNAseq accessions do not make explicit whether the RNA prep was total or polyA. I think TrimGalore and cutadapt require `-a "A{10}"` to...

### Description of feature An idea for a feature request that would be super helpful for plotting and interrogating QC metrics would be to add the QC results as columns...

add --save_merged_fastq for merging technical repeats to fetchngs

5

### Description of feature Hi nfcore/fetchngs team, It would be awesome to add --save_merged_fastq for merging technical repeats to fetchngs. Would be very useful for downstream programs that cant deal...

### Description of the bug Hey, is it intended that `--force_sratools_download` results in different fastq names? Without `--force_sratools_download` the fastqs have naming format `SRX[0-9]+SRR[0-9][1-2].fastq.gz` whereas with `--force_sratools_download` the naming is...

why does input file need to end in .txt

1

### Description of the bug minor point, but why does --input have to match pattern ^\S+\.txt$ Since the input is just a single column of SRR identifiers, it could be...

Concatenate technical repeats

1

### Description of feature When running smrnaseq with technical repeats I get the error: ``` Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT` input file name collision -- There are multiple input files for each of...