rnaseq
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nf-core
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
I think it would be great if the samplesheet could handle additional columns (which would be ignored by the RNA-seq pipeline, but would be used by some downstream analysis). Keeping...
Hello, it looks like TrimGalore does not automatically perform polyA/T removal (see post-trimming fastqc screenshot below) ). They have an experimental option to do so (https://github.com/FelixKrueger/TrimGalore/blob/e9b8fd847f4da01fa3b886d134bc2ecd447a8068/trim_galore#L3230-L3257) but it would require...
## Description of the bug Process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RbohA_KO) terminated with an error exit status (1) Without usefull traces and logs. ## Steps to reproduce Set the current directory to folder...
_From @ewels on March 8, 2017 9:0_ The current MultiQC plot for dupRadar is a little tricky to interpret. Instead of plotting the dotted line from this plot as is...
In issue #420 we had a tricky problem where the featureCounts BioType was creating a biotype entry for every gene. This worked fine, but then caused MultiQC to crash /...
I ran the RNA-seq pipeline on 360 samples, and the slurm submission of multiQC failed with `Pathname of a file, directory or other parameter too long` ``` ERROR ~ Error...
Working on adding the ability for pipeline devs to write nicer / more user friendly error message strings to go into the validation.
I think it may be helpful to include a column in the summary table that shows the number of detected genes for each library. RNA-SeQC output maybe?
Hi I've been getting the following error when working with plant genomes. I've also flagged the error with bx-python (https://github.com/bxlab/bx-python/issues/67): ``` inner_distance.py \ -i Root_1.markdup.sorted.bam \ -r RGT_Planet.bed \ -o...
## Is your feature request related to a problem? Please describe Using nf-test would allow easy local testing for development, and add to the reproducibility with the tests checking for...
