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Issues: DKFZ-ODCF/AlignmentAndQCWorkflows

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45 Open 10 Closed
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Issues list

.DepthOfCoverage_Target.txt has odd output
#90 opened Jan 31, 2024 by vinjana
Get fingerprinting to work with ALT-contig reference
#86 opened Jun 22, 2022 by vinjana
Remove the biobambam sort option
#85 opened May 4, 2022 by vinjana
Add bwa-postalt.js to WGBS bwa job
#84 opened Apr 26, 2022 by vinjana
Move fingerprinting into pipeline
#67 opened Sep 14, 2021 by vinjana
bwa-mem2 support
#66 opened Sep 14, 2021 by vinjana
Check wait -n for task management in bash code
#65 opened Sep 14, 2021 by vinjana
Filename length restriction in R diffchrom script bug Something isn't working
#63 opened Jul 13, 2021 by vinjana
@GWarsow
2
Lift methylation meta job to WFMS level
#62 opened Jun 25, 2021 by vinjana
Calculate target region size from TARGET_REGION_FILE
#58 opened Nov 5, 2019 by vinjana
Tagmentation WGS and WES
#54 opened Jun 26, 2019 by vinjana
Better IO checks in Perl scripts
#53 opened Jun 18, 2019 by vinjana
Merge without duplication marking
#52 opened Jun 18, 2019 by vinjana
Allow setting the number of bases at read start that should should be ignored for conversion statistics
#48 opened Mar 14, 2019 by vinjana
Add collected ambiguously classified undirected WGBS reads in QC-JSON
#47 opened Feb 15, 2019 by vinjana
Move Bash library code to DefaultPlugin or own repo
#46 opened Feb 15, 2019 by vinjana
1
Switch PID registry to associative array
#45 opened Feb 15, 2019 by vinjana
Process data from object storage
#41 opened Jan 16, 2019 by vinjana
Single-end alignment
#40 opened Jan 16, 2019 by vinjana
Make output MultiQC-compatible
#39 opened Jan 16, 2019 by vinjana
Safer online QC statistics on the SAM output stream for post-mortem analysis of alignment (or other processes)
#37 opened Nov 15, 2018 by vinjana
Merge Methylation Calls per library instead of performing methylation calling on merged bam
#36 opened Nov 15, 2018 by vinjana
Handle incremental addition of new lanes when dealing with multiple sequencing libraries
#35 opened Nov 15, 2018 by vinjana
WGBS Bug: coveragePlot.R bug Something isn't working
#33 opened Nov 15, 2018 by vinjana
1
Agglomerate methylation rates over specific sets of chromosomes for QC
#32 opened Nov 15, 2018 by vinjana
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