issues
search
harvardinformatics
/
snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
63
stars
30
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Remove fastq and bam files
#159
max-hence
closed
3 months ago
2
encountered same error when setting cores and executing snpArcher on my local machine
#158
yuan-circle-long
closed
3 months ago
6
Add resources to rules
#157
tsackton
closed
4 months ago
0
Are genotype likelihoods available?
#156
Erythroxylum
closed
4 months ago
1
Update setup.md
#155
cademirch
closed
4 months ago
1
issue with test run
#154
vitorpavinato
closed
4 months ago
11
job execution failed at concat_gvcfs
#153
Erythroxylum
closed
4 months ago
2
Fix typo in mk module
#152
tsackton
closed
4 months ago
0
GATK starts before all bam files are ready
#151
qt37t247
closed
5 months ago
4
update citation
#150
cademirch
closed
5 months ago
0
support snakemake >= 8.0
#149
cademirch
closed
2 months ago
3
Memory allocation problem on a slurm system
#148
Dictionary2b
closed
4 months ago
12
Unable to run test after installation
#147
qt37t247
closed
5 months ago
6
add support for mixed local and sra fastqs
#146
cademirch
closed
5 months ago
0
How to combine NCBI SRA with local data on samplesheet.csv?
#145
Erythroxylum
closed
5 months ago
13
Error in rule create_cov_bed: ModuleNotFoundError: No module named 'pyd4'
#144
Erythroxylum
closed
4 months ago
14
Update write_samples.py
#143
tsackton
closed
6 months ago
0
snakemake doesn't have access to mamba
#142
brian-arnold
closed
3 months ago
4
Unintended whitespace in fastq paths.
#141
ChabbyTMD
closed
7 months ago
5
Error in rule index_reference
#140
ffertrindade
closed
7 months ago
5
add info about starting from bams
#139
cademirch
opened
7 months ago
3
add info about multiple seq runs
#138
cademirch
closed
7 months ago
0
Merge pull request #136 from harvardinformatics/docs
#137
cademirch
closed
7 months ago
0
update docs
#136
cademirch
closed
7 months ago
0
add some doc stuff
#135
cademirch
closed
8 months ago
0
add ploidy options
#134
cademirch
closed
8 months ago
0
add ploidy to haplotype caller
#133
cademirch
closed
8 months ago
1
Python 3.12 seems to break get_reads()
#132
tsackton
closed
7 months ago
0
Update cov_filter.yml
#131
tsackton
closed
8 months ago
3
Update common.smk
#130
erikenbody
closed
8 months ago
0
Update README.md
#129
tsackton
closed
8 months ago
0
Add scaffolds_to_exclude param in QC
#128
aewebb80
closed
8 months ago
4
Update index.md
#127
erikenbody
closed
8 months ago
0
Update setup.md
#126
erikenbody
closed
8 months ago
0
issues during the usage
#125
weirdo-onlooker
closed
9 months ago
1
update read group naming in common.smk
#124
erikenbody
closed
9 months ago
0
Error in rule dedup
#123
weirdo-onlooker
closed
7 months ago
5
Error with qc_admixture rule
#122
ArsenaultResearch
closed
8 months ago
5
Error "incorrect cell order" in gatk_db_import step
#121
reedjohnkenny
closed
7 months ago
6
environment can't be solved
#120
Erythroxylum
closed
9 months ago
5
Error in rule compute_d4
#119
weirdo-onlooker
closed
10 months ago
6
Update path, enable conda
#118
aewebb80
closed
10 months ago
1
Fix mosdepth to 0.3.3 to resolve --d4 issue
#117
aewebb80
closed
10 months ago
3
fix: resource issues #114
#116
cademirch
closed
10 months ago
2
bump bugfix
#115
cademirch
closed
10 months ago
0
Error in rule create_db_intervals
#114
Erythroxylum
closed
10 months ago
12
Trackhubs
#113
cademirch
closed
11 months ago
0
Merge pull request #111 from harvardinformatics/trackhubs
#112
cademirch
closed
11 months ago
0
documenation
#111
cademirch
closed
12 months ago
0
cpus-per-task as required for slurm
#110
erikenbody
closed
2 months ago
3
Previous
Next