epi2me-labs wf-human-variation issues

epi2me-labs / wf-human-variation

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Bamstats version + load container images

#194 hgingras opened 3 days ago
3
Issue with genome build detection

#193 Machadum opened 1 week ago
2
Sniffles failing to complete with no error

#192 parkerpayne opened 2 weeks ago
10
variant calling failed at `concat_refined_snp` step

#191 samuelecancellieri opened 3 weeks ago
1
Missing output file(s) `clair_output/tmp/CHUNK_LIST` expected by process `snp:make_chunks (1)`

#190 nikelau opened 3 weeks ago
1
Big difference between results of qdnaseq and spectre

#189 EugeneKim76 opened 3 weeks ago
1
Missing output file(s) `SAMPLE.haplocheck.tsv` expected by process `haplocheck (1)`

#188 nikelau opened 3 weeks ago
2
Problem while multithreading with slurm

#187 remyvander opened 3 weeks ago
1
Disable automatic Clair3 basecaller lookup

#186 Brynjar-H opened 4 weeks ago
2
Unknown Clair 3 model, (khz prefix)

#185 Brynjar-H closed 4 weeks ago
1
Error executing process > 'mod:modkit_phase (1)'

#184 cihaterdogan opened 1 month ago
23
--sv option fails on v2.2.0 but runs on older versions

#183 graemefox closed 4 weeks ago
8
Spectre CNV results not the same as QDNAseq

#182 charlenelawdes opened 1 month ago
1
Failed phasing for SV

#181 agatafant closed 4 weeks ago
1
to_delete

#180 selmapichot closed 1 month ago
1
Understanding Blue, Underlined Reads in `samtools view` Output for CNV Regions

#179 ParkShinHyun closed 1 month ago
1
add option to force re-alignment

#178 flokraft85 opened 1 month ago
1
specified genome fasta is not used for alignment

#177 flokraft85 closed 1 month ago
1
Explicit support for SLURM and other schedulers

#176 adbeggs closed 2 months ago
3
error pulling singularity image

#175 selmapichot opened 2 months ago
6
error pulling singularity image

#174 selmapichot closed 2 months ago
1
cannot detect snv with adaptive sampling

#173 dhlee3342 closed 2 months ago
2
The genome build detected in the BAM is not compatible with this workflow.

#172 selmapichot closed 2 months ago
6
Can CNV calling via Spectre run without --snv?

#171 SkabbiVML closed 2 months ago
3
What's new in sniffles-2.0.7-epime?

#170 ymcki closed 2 months ago
2
Enable running --str (or other subcomponents of the pipeline) more modularly

#169 ilivyatan opened 2 months ago
1
nf-core failure to attain singularity containers

#168 bcardus closed 1 month ago
2
cnv_spectre: callCNV gets stuck

#167 ilivyatan closed 1 month ago
5
Process `getGenome (1)` terminated with an error exit status

#166 Aravind-mss closed 2 months ago
8
Error executing process 'cnv_spectre:makeReport (1)'

#165 cihaterdogan closed 1 month ago
3
snpeff fails with segfault

#164 trum994 opened 3 months ago
7
wrong STR thresholds in STR-report

#163 tamara-nano closed 1 month ago
3
dbNSFP for snps annotation

#162 blanleung closed 2 weeks ago
2
FATAL: Relocation not allowed with starter-suid

#161 blanleung closed 3 months ago
3
Does the phasing run despite the configuration not to run phasing?

#160 ilivyatan closed 2 months ago
3
.apptainer/cache

#159 selmapichot closed 3 months ago
2
CRAM or BAM output

#158 asalhab closed 3 months ago
1
Annotating common variants with SnpSift annotate within wf-human-variation workflow

#157 litte024 closed 2 weeks ago
4
How do I find out which version has been used?

#156 sklages closed 1 month ago
4
PCR duplicates removal

#155 seven1112233 closed 3 months ago
1
snp:evaluate_candidates Aborted

#154 gdemoro closed 1 month ago
3
Specifying bin_size for Spectre cnv

#153 fidibidi closed 3 months ago
1
Calling SV/SNP when using a bam file generated with a remora_cfg

#152 fidibidi closed 3 months ago
1
--mod and --cnv output files seemingly missing or labelled incorrectly?

#151 fidibidi closed 3 months ago
3
About minimum cpu requirement

#150 AlbertoOsorio closed 1 month ago
1
Error at aggregating and sorting pileup variants, no 'pileup.vcf.gz' as output

#149 Krysasp opened 3 months ago
1
Speeding up snp variant calling?

#148 Krysasp closed 4 months ago
1
Update wf-human-variation in an environment without internet access

#147 ParkShinHyun closed 4 months ago
1
For non-model reference genome?

#146 CWYuan08 closed 1 month ago
10
minimap2 alignment step fails because of samtools sort

#145 trum994 opened 4 months ago
5