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NBISweden
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GenErode
GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Smaller bug fixes
#34
verku
closed
1 year ago
0
Update cluster.yaml
#33
verku
closed
1 year ago
0
Rerun issue with snakemake 7.8
#32
lored322
closed
1 year ago
2
Issues with cookiecutter in UPPMAX
#31
jcchacond
closed
1 year ago
2
Singularity issue?
#30
ndussex
closed
1 year ago
4
fastp can get memory issues
#29
verku
opened
1 year ago
0
Upgrade to Snakemake version 7 and leaving python version open
#28
verku
closed
1 year ago
0
Upgrade to Snakemake version 7
#27
verku
closed
1 year ago
1
Rewrite memory allocation for java-based tools (e.g. qualimap)
#26
verku
opened
1 year ago
0
Re-run incomplete warning for rule make_reference_bed
#25
verku
closed
1 year ago
0
snpEff prepare_db_build does not recognize file type
#24
verku
closed
1 year ago
1
Merge changes from dev into main for version 0.4.2
#23
verku
closed
1 year ago
0
Add docker images combining bedtools and bgzip and update code to compress filtered vcf files (issue #19)
#22
verku
closed
1 year ago
0
SnpEff using -Xmx for large genomes, closing issue #14
#21
verku
closed
2 years ago
0
Temp cluster
#20
verku
closed
2 years ago
0
compressing vcf file (rule remove_CpG_vcf - 8.1_vcf_CpG_filtering.smk)
#19
ndussex
closed
1 year ago
1
Remove temp flag for rescaled bam *.bai files
#18
verku
closed
1 year ago
0
Update conda in github actions with setup-miniconda from conda-incubator
#17
verku
closed
2 years ago
0
Mitogenomes
#16
verku
closed
1 year ago
1
Missing input files error for group job in mitogenome mapping step
#15
verku
closed
1 year ago
3
snpEff build fails with "Out of memory"
#14
verku
closed
1 year ago
0
Mutational load plot y-axis label overlaps with y-axis tick labels
#13
verku
closed
1 year ago
1
Update documentation
#12
verku
closed
2 years ago
0
Cluster config updates
#11
verku
closed
1 year ago
0
Minor formatting
#10
verku
closed
2 years ago
0
Revert "Bug fixes and minor updates for v0.4.1"
#9
verku
closed
2 years ago
0
Bug fixes and minor updates for v0.4.1
#8
verku
closed
2 years ago
0
Github actions: replace conda with a faster implementation
#7
verku
closed
1 year ago
0
Pipeline report: image embedding
#6
verku
closed
1 year ago
1
Fix indentation error
#5
verku
closed
2 years ago
0
Github actions failure: indentation wrong in if/else clauses
#4
verku
closed
1 year ago
0
Implement shadow rules for some rules (e.g. repeatmodeler)
#3
verku
opened
2 years ago
2
Add some basic statistics on GERP scores to pipeline report for threshold decisions
#2
verku
opened
2 years ago
0
Make threshold for Froh calculations adjustable in configuration
#1
verku
opened
2 years ago
0
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