DKFZ-ODCF AlignmentAndQCWorkflows issues

DKFZ-ODCF / AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows/wiki

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Roddy cannot zip folder

#91 AndreasKienzle opened 5 months ago
0
`.DepthOfCoverage_Target.txt` has odd output

#90 vinjana opened 9 months ago
0
fix filename length restriction

#89 GWarsow closed 1 year ago
2
Remove named pipes

#88 vschnei closed 1 year ago
0
Draft: Fix memory problem with alt hla

#87 vinjana opened 1 year ago
1
Get fingerprinting to work with ALT-contig reference

#86 vinjana opened 2 years ago
0
Remove the biobambam sort option

#85 vinjana opened 2 years ago
0
Add bwa-postalt.js to WGBS bwa job

#84 vinjana opened 2 years ago
0
Bwa postalt.js update

#83 vinjana closed 2 years ago
0
Bwa postalt.js update

#82 vinjana closed 2 years ago
0
Draft: BWA MEM 2 support

#81 vinjana opened 2 years ago
3
Bwa mem2

#80 vinjana closed 2 years ago
0
Use bwa-postalt.js postprocessing for alignment against hg38 with ALT contigs

#79 vinjana closed 2 years ago
4
Configuration summary script for this workflow.

#78 vinjana closed 1 year ago
1
Added Python script to create adapter files for Trimmomatic.

#77 vinjana closed 2 years ago
5
Move fingerprinting into pipeline

#67 vinjana opened 3 years ago
0
bwa-mem2 support

#66 vinjana opened 3 years ago
0
Check wait -n for task management in bash code

#65 vinjana opened 3 years ago
0
Fix issue 63: filename length bug

#64 GWarsow closed 3 years ago
0
Filename length restriction in R diffchrom script

#63 vinjana opened 3 years ago
2
Lift methylation meta job to WFMS level

#62 vinjana opened 3 years ago
0
_de novo_ adapter detection

#60 vinjana closed 1 year ago
1
Added MBUFFER_VERSION and module loading to correct 2018/2016 mbuffer…

#59 vinjana closed 4 years ago
0
Calculate target region size from TARGET_REGION_FILE

#58 vinjana opened 5 years ago
0
An interface change in newer (at least 20190725) version of mbuffer c…

#57 vinjana closed 5 years ago
0
mbuffer as module

#56 vinjana closed 5 years ago
1
Patch to test out sleep (timing change) and better error checks in filter_readbins.pl

#55 vinjana closed 5 years ago
0
Tagmentation WGS and WES

#54 vinjana opened 5 years ago
0
Better IO checks in Perl scripts

#53 vinjana opened 5 years ago
0
Merge without duplication marking

#52 vinjana opened 5 years ago
0
Refactorings in 1.2.73 release branch, mostly BWA top-level job scripts

#51 vinjana closed 5 years ago
0
Fixed a div/0 error that occured with a low-coverage sample.

#50 vinjana closed 5 years ago
0
Migrate docu to wiki

#49 vinjana closed 5 years ago
0
Allow setting the number of bases at read start that should should be ignored for conversion statistics

#48 vinjana opened 5 years ago
0
Add collected ambiguously classified undirected WGBS reads in QC-JSON

#47 vinjana opened 5 years ago
0
Move Bash library code to DefaultPlugin or own repo

#46 vinjana opened 5 years ago
1
Switch PID registry to associative array

#45 vinjana opened 5 years ago
0
Add for-loop to waitForRegisteredPids

#44 vinjana closed 5 years ago
0
Unidirectional wgbs read reordering

#43 vinjana closed 5 years ago
0
Undirectional WGBS read reordering

#42 vinjana closed 5 years ago
1
Process data from object storage

#41 vinjana opened 5 years ago
0
Single-end alignment

#40 vinjana opened 5 years ago
0
Make output MultiQC-compatible

#39 vinjana opened 5 years ago
0
Some fixes

#38 vinjana closed 5 years ago
0
Safer online QC statistics on the SAM output stream for post-mortem analysis of alignment (or other processes)

#37 vinjana opened 6 years ago
0
Merge Methylation Calls per library instead of performing methylation calling on merged bam

#36 vinjana opened 6 years ago
0
Handle incremental addition of new lanes when dealing with multiple sequencing libraries

#35 vinjana opened 6 years ago
0
WGBS: Include Option for non-directional protocol

#34 vinjana closed 5 years ago
0
WGBS Bug: coveragePlot.R

#33 vinjana opened 6 years ago
1
Agglomerate methylation rates over specific sets of chromosomes for QC

#32 vinjana opened 6 years ago
0