BIMSBbioinfo pigx_bsseq issues

BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

https://bioinformatics.mdc-berlin.de/pigx/

GNU General Public License v3.0

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issues

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Make backwards compatible

#197 alexg9010 closed 6 days ago
0
Update build.yml

#194 alexg9010 closed 1 week ago
0
[export_tbx2bw] skip chromosomes without mapping

#193 alexg9010 closed 1 week ago
0
Error in getTabixByChunk

#190 fafaris39 opened 1 year ago
1
clean/reports

#189 alexg9010 closed 1 week ago
0
possibility to quickly rerun given target, without all upstream rules

#188 alexg9010 opened 1 year ago
0
forced rerun not possible with write-protected output

#187 alexg9010 opened 1 year ago
0
steps to run make distcheck via Github actions take quite long with caching

#186 alexg9010 opened 1 year ago
3
Consider option to add spike-in genome for calculation of bisulfite conversion rate

#185 alexg9010 opened 1 year ago
0
Catch error during final report rendering when refgene and cpgislandfile are not given

#184 alexg9010 opened 1 year ago
0
Missing pigx-common file in source installation

#183 AnjaCaRa closed 1 year ago
1
Use `asis` engine for conditional printing of markdown chunks

#182 alexg9010 opened 1 year ago
0
m4/ax_r_package.m4 is outdated

#181 rekado closed 2 years ago
0
try unit test generation feature of snakemake

#180 alexg9010 opened 2 years ago
0
describe how to get gene prediction files from ucsc table browser or link to source where it is described

#179 alexg9010 opened 2 years ago
0
allow users to fetch other ucsc gene prediction tables

#178 alexg9010 opened 2 years ago
0
rename targets to rule names

#177 alexg9010 opened 2 years ago
1
collate targets to workflows

#176 alexg9010 opened 2 years ago
0
improve the printing of available targets

#175 alexg9010 opened 2 years ago
0
Skip check for Bisulfite Genome Folder if use_bismark is false

#174 alexg9010 opened 2 years ago
0
Update manual on github

#173 katwre opened 2 years ago
1
if diffmeth section is commented out, leads to error

#172 alexg9010 opened 2 years ago
1
evaluate switch from trim galore to fastp read trimming

#171 alexg9010 opened 3 years ago
1
pre-screening to figure out the required settings

#170 alexg9010 opened 3 years ago
0
error when destranding during exporting bigwig

#169 alexg9010 opened 3 years ago
0
Use shared runner template

#168 rekado closed 3 years ago
0
Describe format of DMR bed files in report and/or docs

#167 alexg9010 opened 3 years ago
0
Missing chromosomal position in mthyl call

#166 devenderarora opened 3 years ago
5
update guix.scm

#165 alexg9010 closed 3 years ago
2
"make check" fails (out of memory?)

#164 rekado opened 3 years ago
1
Allow covariates for differential analysis

#163 alexg9010 opened 4 years ago
0
Fix case where target=posttrim-qc

#162 Blosberg closed 3 years ago
1
Tests fail on bwameth_align_trimmed

#161 Blosberg opened 4 years ago
4
Add a YAML schema for validation

#160 alexg9010 opened 4 years ago
0
Add bwa meth

#159 alexg9010 closed 4 years ago
0
Error generating diffmeth reports

#158 srikanthkris closed 4 years ago
2
add compression of bam to cram for unused bam files

#157 alexg9010 opened 4 years ago
0
add methylation difference bigwig track

#156 alexg9010 opened 4 years ago
0
change the score in dmc bed to integer format

#155 alexg9010 opened 4 years ago
0
Calculate conversion rate from mBias file

#154 alexg9010 opened 4 years ago
0
reduce number of final bam files

#153 alexg9010 opened 4 years ago
0
add bwa meth branch for the workflow

#152 alexg9010 closed 4 years ago
1
use methylDackel for methylation extraction

#151 alexg9010 closed 4 years ago
0
use sambamba for markduplicates

#150 alexg9010 closed 4 years ago
4
add bitmapper as aligner option

#149 alexg9010 opened 4 years ago
0
Raw QC dependent on trimming

#148 alexg9010 closed 4 years ago
2
Inlcude thread settings for bowtie2 instances

#147 alexg9010 closed 11 months ago
5
treatment groups have to be in quotes

#146 alexg9010 closed 4 years ago
0
pigx_bsseq for RRBS

#145 xie186 closed 4 years ago
1
Error message from "guix install pigx-bsseq"

#144 xie186 closed 4 years ago
2