nf-core viralrecon issues

nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

https://nf-co.re/viralrecon

MIT License

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issues

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Bump fastqc

#436 Joon-Klaps closed 10 hours ago
1
Changed Cutadapt to use nf-core modules

#435 svarona opened 2 weeks ago
1
Enhanced BLAST results filtering

#434 svarona closed 2 weeks ago
1
Update MultiQC

#433 maxulysse opened 3 weeks ago
1
Include lofreq module, and merge lofreq and ivar results

#432 shesanIsland opened 3 weeks ago
0
Old container for FASTQC processes in current release (2.6.0) is old and now fails on AWS Batch

#431 FloWuenne closed 10 hours ago
4
Template update for nf-core/tools version 2.14.1

#430 svarona closed 3 weeks ago
1
variant discrepancy between in ivar and snpeff annotated file

#429 wantingwei opened 1 month ago
2
Important! Template update for nf-core/tools v2.14.1

#428 nf-core-bot closed 3 weeks ago
0
Important! Template update for nf-core/tools v2.14.0

#427 nf-core-bot closed 1 month ago
1
417 allow skipping freyja boot

#426 Joon-Klaps closed 1 month ago
6
ivariant filtering problem using 'tsv file' generated by 'ivar variant' command.

#425 Moslemecoh closed 1 month ago
7
Template update for nf-core/tools v2.13.1

#424 svarona closed 2 months ago
2
Error when running illumina command

#423 fractaljc opened 2 months ago
0
nf-core/viralrecon run halted due to R version clash

#422 asanenjoy opened 3 months ago
5
Important! Template update for nf-core/tools v2.13.1

#421 nf-core-bot closed 2 months ago
0
Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking

#420 ddomman opened 4 months ago
4
`MOSDEPTH_AMPLICON` doesn't run in `dev` branch

#419 tavareshugo closed 2 months ago
1
Important! Template update for nf-core/tools v2.13

#418 nf-core-bot closed 4 months ago
0
Allow skipping `freyja boot`

#417 tavareshugo closed 1 month ago
1
Template update for nf-core/tools version 2.12

#416 svarona closed 4 months ago
1
Temp file problem in VARIANTS_IVAR:BCFTOOLS_SORT

#415 Paururo opened 5 months ago
1
Important! Template update for nf-core/tools v2.12

#414 nf-core-bot closed 4 months ago
1
Update multiqc & add freyja to MQC

#413 Joon-Klaps closed 5 months ago
5
Add parameter freyja_depthcutoff

#412 Joon-Klaps closed 5 months ago
4
Properly deal with multiqc in the config files before the next release

#411 maxulysse opened 5 months ago
3
Test for medaka model

#410 svarona closed 5 months ago
1
Make cutadapt primer's position ext.arg

#409 svarona opened 5 months ago
0
Fixed conflicts and updated modulels for nf-core/tools version 2.11.1

#408 svarona closed 5 months ago
7
Important! Template update for nf-core/tools v2.11.1

#407 nf-core-bot closed 5 months ago
1
Important! Template update for nf-core/tools v2.11

#406 nf-core-bot closed 6 months ago
1
Adding "--grouplineages" parameter in the nf-core/viralrecon

#405 bsalehe closed 5 months ago
3
Split authors in generated RO crate

#404 renatocjn opened 7 months ago
0
Unable to download the python script

#403 Mahendra687 closed 1 month ago
3
Error running version 2.6.0 with Nanopore data in process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION

#402 AdrianMBarrera opened 8 months ago
0
Added option to add a custom annotation, clarified multiQC results and fixed issues

#401 svarona closed 2 months ago
2
Adding "aggregate" and "plot" methods in the freyja subworkflow

#400 bsalehe closed 5 months ago
4
Problem installing viralrecon

#399 vilocha opened 8 months ago
0
Argument input-fasta is missing in NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:NEXTCLADE_RUN"

#398 CeliaRodrigues opened 8 months ago
4
Important! Template update for nf-core/tools v2.10

#397 nf-core-bot closed 6 months ago
1
Apply samtools fixmate after ivar trim

#396 wutron opened 9 months ago
1
Remove minia from default assembler

#395 adamrtalbot closed 9 months ago
2
Add QIAseq DIRECT SARS-CoV-2 Kit amplicons

#394 dwinter opened 10 months ago
0
Changed primer set to params

#393 svarona closed 5 months ago
2
Artic v5 mismatched primer names in artic-ncov2019 repo cause certain amplicons to be erroneously filtered/removed

#392 Sam-Sims opened 10 months ago
0
primer_set is not taking param

#391 svarona closed 3 months ago
0
Allow viralrecon to take gtf as input annotation file

#390 svarona closed 2 months ago
0
epi2me-labs/wf-cnv failed during analysis

#389 Ligerd5 closed 10 months ago
7
adding fastqc trimmed in report

#388 Joon-Klaps closed 11 months ago
2
Remove system exit 1

#387 adamrtalbot closed 10 months ago
1