BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

BIMSBbioinfo/pigx_rnaseq Issues

Copy/link the annotation in the results folder
Closed 8 months ago
yieldSize hardcoded in count_reads.R
Closed 8 months ago
Error when submitting to cluster
Closed 8 months ago21
Collating Salmon counts fails
Closed 8 months ago
error when executing
Closed 2 years ago3
salmon results show no gene names - with latest guix rnaseq 0.1
Updated 2 years ago6
add a module for gene-set enrichment analysis
Updated 2 years ago
Rule specific memory requirements are not respected in cluster submission
Updated 2 years ago7
suggesting runtime tests
Updated 2 years ago4
all rules should have `resources`
Closed 2 years ago4
update settings template to include log-dir option
Closed 2 years ago
suggesting singularity image
Closed 2 years ago3
samtools: files already existing
Closed 2 years ago3
remove leading and trailing whitespaces from given target list
Updated 2 years ago2
counts from salmon fails for single sample
Updated 2 years ago1
Analysis name in "DEanalyses" section must be quoted
Updated 2 years ago1
counts from salmon fails if sample_type is empty
Closed 2 years ago1
crash when sample sheet contains empty lines
Closed 2 years ago1
add megadepth for fast genome coverage computation
Closed 2 years ago2
suggesting check of covariates against sample sheet column names
Closed 2 years ago
'group_by' applied to an object of class "c('plotly', 'htmlwidget') - anyone?
Closed 2 years ago9
counts from salmon / tximport crash when adding new samples to project
Closed 2 years ago6
Slurm as a queuing system for pigx-rnaseq? Or generally abstract away from gridengine?
Closed 2 years ago2
sample_sheets - accept experiments without a fastq file referenced
Closed 2 years ago3
gprofiler2 report not shown with DT::datatable
Closed 2 years ago8
'pandoc-citeproc' not in requirements
Closed 2 years ago1
Outdated m4/ax_r_package.m4
Closed 2 years ago1
default settings.yaml lacks 'log-dir' specification
Closed 3 years ago3
Code shown in Report does not define "params"
Closed 3 years ago2
Multiple fastq input files per sample?
Closed 3 years ago3
Paired analyses?
Closed 3 years ago2
Spreadsheet-generated sample_sheet not properly importable - early warning?
Closed 3 years ago7
hisat2-build expects fasta file, doe not accept fasta.gz - maybe warn earlier?
Closed 3 years ago2
Check for blanks in filename when samples are not found
Closed 3 years ago4
Allow pre-built genome indices as input
Updated 3 years ago
CI tests with Debian?
Updated 3 years ago2
upgrade gprofiler to gprofiler2
Closed 3 years ago
It's the memory, stupid! How to solve the "cannot change locale" problem.
Closed 3 years ago7
MissingOutputException for "samtools index" with 0.0.13
Closed 3 years ago2
replace export.bw with a better candidate
Closed 3 years ago2
RNA-Seq pipeline stopping after trim galore
Closed 3 years ago1
Replace trimgalore with bbtrim
Closed 3 years ago2
Implement a secondary mapper with lower memory footprint
Closed 3 years ago4
DEanalysis covariates should not be manadatory
Closed 3 years ago5
STAR - unknown parameter genomeType - after guix install pigx-rnaseq
Closed 3 years ago5
Allow configuration of STAR parameter --limitGenomeGenerateRAM
Closed 3 years ago3
test.sh on trimmed_reads misses file after successful execution
Closed 4 years ago1
Use Drimseq for differential transcript analysis
Updated 4 years ago
File names ending in .fq.gz crash trim_galore rule
Closed 4 years ago
catching missing qsub error
Updated 4 years ago