BIMSBbioinfo pigx_rnaseq issues

BIMSBbioinfo / pigx_rnaseq

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

GNU General Public License v3.0

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issues

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added rounding in dynamic resource specification

#150 FrancescoSantini closed 2 months ago
0
dynamic requirements for some rules

#149 FrancescoSantini closed 3 months ago
0
Revert "added resource request for AWS"

#148 alexg9010 closed 3 months ago
0
added resource request for AWS

#147 FrancescoSantini closed 3 months ago
0
DESeq2 checkFullRank() fails with no directions where to look

#146 smoe opened 5 months ago
3
`record_annotation_files` uses uncaptured tools

#145 rekado opened 6 months ago
1
Tibanna

#144 rekado closed 6 months ago
0
Fix for issue#140

#143 FrancescoSantini closed 7 months ago
1
Changing the cDNA fasta should not trigger rerun of hisat2 branch

#142 alexg9010 opened 7 months ago
0
Local build of pipeline fails to run on cluster

#141 alexg9010 opened 8 months ago
2
Pipeline fails on settings file without DEA when trying to collate deseq reports

#140 alexg9010 closed 7 months ago
3
Issues/138

#139 alexg9010 closed 8 months ago
1
Fix mismatching names for cluster config and Snakefile

#138 alexg9010 closed 8 months ago
6
Pandoc error when running using cluster submission

#137 alexg9010 opened 8 months ago
6
Added short script to collate deseq_results.tsv from all the differen…

#136 FrancescoSantini closed 9 months ago
0
Collating Salmon counts fails

#135 borauyar closed 1 year ago
0
Copy/link the annotation in the results folder

#134 frenkiboy closed 1 year ago
0
Error when submitting to cluster

#133 Pinolinoo closed 1 year ago
21
error when executing

#132 Pinolinoo closed 2 years ago
3
yieldSize hardcoded in count_reads.R

#131 kerimsecener closed 1 year ago
0
salmon results show no gene names - with latest guix rnaseq 0.1

#130 smoe opened 2 years ago
6
add a module for gene-set enrichment analysis

#129 borauyar opened 2 years ago
0
Rule specific memory requirements are not respected in cluster submission

#128 borauyar closed 8 months ago
12
suggesting singularity image

#127 smoe closed 2 years ago
3
suggesting runtime tests

#126 smoe opened 2 years ago
4
Outdated m4/ax_r_package.m4

#125 tillea closed 2 years ago
1
scripts/collate: header is always needed, not 'auto'

#124 smoe closed 2 years ago
1
samtools: files already existing

#123 smoe closed 2 years ago
3
suggesting check of covariates against sample sheet column names

#122 smoe closed 2 years ago
0
Passing 'selfContained' as parameter

#121 smoe closed 2 years ago
3
Passing description from settings.yaml to report.

#120 smoe closed 3 years ago
2
gprofiler2 report not shown with DT::datatable

#119 smoe closed 2 years ago
8
Helping local execution of code producing figures

#118 smoe closed 3 years ago
2
sample_sheets - accept experiments without a fastq file referenced

#117 smoe closed 2 years ago
3
idea how to print instruction to directly set paths to reproduce analysis

#116 smoe closed 3 years ago
2
Code shown in Report does not define "params"

#115 smoe closed 3 years ago
2
Paired analyses?

#114 smoe closed 3 years ago
2
Avoid runtime error during merge, no headers in table

#113 smoe closed 3 years ago
6
default settings.yaml lacks 'log-dir' specification

#112 smoe closed 3 years ago
3
Spreadsheet-generated sample_sheet not properly importable - early warning?

#111 smoe closed 3 years ago
7
Slurm as a queuing system for pigx-rnaseq? Or generally abstract away from gridengine?

#110 smoe closed 2 years ago
2
Warn about genome reference data remaining compressed

#109 smoe closed 3 years ago
1
Detecting blanks in flanks of samples' filenames

#108 smoe closed 3 years ago
1
hisat2-build expects fasta file, doe not accept fasta.gz - maybe warn earlier?

#107 smoe closed 3 years ago
2
Check for blanks in filename when samples are not found

#106 smoe closed 3 years ago
4
Multiple fastq input files per sample?

#105 smoe closed 3 years ago
3
'pandoc-citeproc' not in requirements

#104 robert-altwasser closed 2 years ago
1
all rules should have `resources`

#103 rekado closed 2 years ago
4
add megadepth for fast genome coverage computation

#102 borauyar closed 2 years ago
2
update settings template to include log-dir option

#101 borauyar closed 2 years ago
0