nf-core pathogensurveillance issues

nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

https://nf-co.re/pathogensurveillance

MIT License

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issues

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Replace `VCF_TO_TAB` and `VCF_TO_SNPALN` with a single R script or other command

#122 zachary-foster opened 23 hours ago
0
ASSIGN_CONTEXT_REFERENCES error

#121 cahuparo opened 1 day ago
1
Consider changing MSN threshold to number of SNPs

#120 zachary-foster opened 2 days ago
0
Add scale bars to trees

#119 zachary-foster opened 2 days ago
0
BUSCO error = BrokenPipeError: [Errno 32] Broken pipe

#118 cahuparo opened 3 days ago
0
Name dropdown entires for MSN by reference taxon name

#117 zachary-foster opened 3 days ago
0
Consider the abundance of the taxon when choosing references.

#116 zachary-foster opened 3 days ago
0
Add option to specify number of replicates when downloading references

#115 zachary-foster opened 3 days ago
0
accept assemblies as well as reads

#114 cahuparo opened 1 week ago
0
Switch from `entrez` commands to `datasets` commands for downloading assembly metadata

#113 zachary-foster opened 2 weeks ago
0
Sometimes "find_assemblies" returns an empty table without an error

#112 zachary-foster closed 2 weeks ago
1
Dont run VARIANT_ANALYSIS subworkflow for groups with less than 2 samples

#111 zachary-foster closed 2 weeks ago
0
FASTP error: input files don't contain identical amount of reads

#110 cahuparo closed 2 weeks ago
3
Out of date spades may be causing errors with assemblies

#109 cahuparo opened 2 weeks ago
2
Double quotes in queries in input causes parsing errors with the new nf-core template

#108 zachary-foster opened 3 weeks ago
0
Add a way to extract SRA ids from NCBI/ENA biosample ids

#107 cahuparo closed 3 weeks ago
0
Template merge

#106 zachary-foster closed 3 weeks ago
0
Add module to check quality of Spades assembly

#105 logankblair opened 3 weeks ago
0
Change assign_context_references.R to give more informative error message

#104 logankblair opened 3 weeks ago
0
Failed rendering report

#103 buchanri opened 4 weeks ago
2
fix nextflow schema formatting

#102 mashehu closed 1 month ago
4
When all samples have only exclusive user-defined references. the pipeline breaks

#101 zachary-foster closed 3 weeks ago
1
Add header to FIND_ASSEMBLIES output

#100 zachary-foster opened 1 month ago
0
VCF_CONCATENATE cannot be called on long references

#99 zachary-foster closed 1 month ago
0
assign_mapping_reference not being cached

#98 zachary-foster closed 2 weeks ago
1
Important! Template update for nf-core/tools v3.0.2

#97 nf-core-bot closed 3 weeks ago
0
Important! Template update for nf-core/tools v3.0.1

#96 nf-core-bot closed 1 month ago
1
Important! Template update for nf-core/tools v3.0.0

#95 nf-core-bot closed 1 month ago
1
Error when some assembly metadata tsv files are empty and don't contain accessions to download

#94 masudermann opened 2 months ago
0
Unable to finish picking assemblies

#93 buchanri closed 1 month ago
0
Large and complex test data set

#92 zachary-foster closed 2 weeks ago
1
Add maximum file size parameter to filtered downloaded assemblies and reads

#91 zachary-foster opened 3 months ago
0
Bakta database bug ("amrfinder error")

#90 zachary-foster closed 2 weeks ago
1
Error rendering report when I don't have core gene phylogeny (eukaryote dataset)

#89 masudermann closed 3 weeks ago
3
Update from grunwaldlab fork

#88 zachary-foster closed 3 months ago
0
Fail to create conda environment for sourmash_sketch

#87 buchanri opened 4 months ago
1
Looking for sample sheet metadata not in the provided path

#86 buchanri closed 3 weeks ago
1
BBmap_Sendsketch not finding SRA

#85 buchanri opened 4 months ago
0
Use web history for large NCBI queries to enable downloading of >300 samples

#84 zachary-foster closed 4 months ago
1
Sample sheet error

#83 buchanri closed 3 weeks ago
1
read2tree issue on mixed dataset

#82 masudermann closed 2 weeks ago
1
Error when testing xanthomonas small dataset

#81 buchanri closed 3 weeks ago
1
Add subsetting of variants when there are more than a user-defined maximum

#80 zachary-foster opened 4 months ago
0
Make SUBSET module name its output by the sample ID

#79 zachary-foster opened 5 months ago
0
Make DOWNLOAD_ASSEMBLIES store data more effeciently

#78 zachary-foster closed 3 weeks ago
1
BUSCO graphs for assembled genomes

#77 grunwald opened 5 months ago
2
We need to review the step where we convert Graphtyper VCF outputs files to tabular format using vcf-to-tab

#76 masudermann opened 5 months ago
1
Report fails to render if I don't have POCP matrix-an issue when dealing with eukaryotic datasets

#75 masudermann opened 5 months ago
0
Killed with a warning?

#74 cahuparo closed 3 weeks ago
0
Allow users to define custom references for phylogenies

#73 zachary-foster closed 4 months ago
1