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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Error when some assembly metadata tsv files are empty and don't contain accessions to download

#94 masudermann opened 1 week ago
0
Unable to finish picking assemblies

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

#92 zachary-foster opened 1 month ago
0
Add maximum file size parameter to filtered downloaded assemblies and reads

#91 zachary-foster opened 1 month ago
0
Bakta database bug ("amrfinder error")

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

#89 masudermann opened 1 month ago
2
Update from grunwaldlab fork

#88 zachary-foster closed 2 months ago
0
Fail to create conda environment for sourmash_sketch

#87 buchanri opened 2 months ago
1
Looking for sample sheet metadata not in the provided path

#86 buchanri opened 2 months ago
1
BBmap_Sendsketch not finding SRA

#85 buchanri opened 2 months ago
0
Use web history for large NCBI queries to enable downloading of >300 samples

#84 zachary-foster closed 2 months ago
1
Sample sheet error

#83 buchanri opened 2 months ago
1
read2tree issue on mixed dataset

#82 masudermann opened 2 months ago
0
Error when testing xanthomonas small dataset

#81 buchanri opened 2 months ago
0
Add subsetting of variants when there are more than a user-defined maximum

#80 zachary-foster opened 3 months ago
0
Make SUBSET module name its output by the sample ID

#79 zachary-foster opened 3 months ago
0
Make DOWNLOAD_ASSEMBLIES store data more effeciently

#78 zachary-foster opened 3 months ago
0
BUSCO graphs for assembled genomes

#77 grunwald opened 4 months ago
1
We need to review the step where we convert Graphtyper VCF outputs files to tabular format using vcf-to-tab

#76 masudermann opened 4 months ago
1
Report fails to render if I don't have POCP matrix-an issue when dealing with eukaryotic datasets

#75 masudermann opened 4 months ago
0
Killed with a warning?

#74 cahuparo opened 4 months ago
0
Allow users to define custom references for phylogenies

#73 zachary-foster closed 3 months ago
1
Important! Template update for nf-core/tools v2.14.1

#72 nf-core-bot opened 4 months ago
0
Important! Template update for nf-core/tools v2.14.0

#71 nf-core-bot closed 4 months ago
1
Graphtyper flag may need to be added if working with Nanopore data otherwise empty merged vcf file

#70 masudermann opened 5 months ago
4
Mixed dataset issue-BBsketch misclassified one sample as a pseudomonad rather than nematode and spades ran out of memory

#69 masudermann closed 5 months ago
1
If I want to include a long read accession from NCBI, is there a way to detect that reads are long and not short?

#68 masudermann closed 3 months ago
1
pathogensurveillance.nf error before picard step

#67 logankblair closed 5 months ago
4
Error rendering final report

#66 logankblair closed 5 months ago
7
When only SRA accessions are provided in metadata input file, what happens if both SE and PE fastq reads are downloaded for particular accession?

#65 masudermann closed 4 months ago
1
README enhancements

#64 zachary-foster opened 5 months ago
0
Add option to delete or not publish intermendiate files

#63 zachary-foster closed 3 months ago
3
Make input CSV column names and some value case insensitive and spaces = underscores

#62 zachary-foster closed 5 months ago
1
Check if type strains are being chosen for references

#61 zachary-foster opened 5 months ago
0
Variant calling uses alternate reference but retains user-defined reference id

#60 cahuparo opened 5 months ago
0
PATHOGENSURVEILLANCE:RECORD_MESSAGES process not finished but pipeline says it completed successfully

#59 masudermann closed 5 months ago
1
Docker bwa image no longer loading for docker version 25+

#58 logankblair opened 5 months ago
0
read2tree formater ready

#57 ricardoi closed 3 months ago
1
Check if we need to add quality filtering of flye assemblies of nanopore/pacbio

#56 zachary-foster closed 5 months ago
1
Add input column to define type of nanopore/pacbio sequencing

#55 zachary-foster opened 5 months ago
0
Add a check to the input to ensure only one type of sequence data is present for each sample

#54 zachary-foster closed 5 months ago
1
Add code to check what type of sequencing is downloaded from the SRA (Illumina, nanopore, pacbio, etc)

#53 zachary-foster closed 3 months ago
1
If there are no variants print a warning message in messages.tsv

#52 zachary-foster opened 5 months ago
0
If Spades or Bakta fail for small number of samples, is there a way to proceed without these samples?

#51 masudermann opened 5 months ago
0
Including number of genes and SNPs used to build trees

#50 upasana3 opened 6 months ago
1
If there are no messages, then the report is not made

#49 zachary-foster closed 6 months ago
1
Add tmp dir argument to picardtools sortsam

#48 upasana3 closed 6 months ago
1
Sample sheet does not appear to contain a header

#47 bark9299 closed 4 months ago
1
ASSIGN_REFERENCES:SOURMASH_COMPARE error when inputting newly formatted test metadata file

#46 masudermann closed 3 months ago
4
Test data does not match the input check requirements

#45 cahuparo closed 7 months ago
2