czbiohub-sf sc2-illumina-pipeline issues

czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

GNU Affero General Public License v3.0

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issues

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coverage plot per pool

#86 aspitaleri opened 2 years ago
0
duplicate in bam

#85 aspitaleri opened 3 years ago
2
trimReads fails: no file sample1_artic_R_covid_1_val_1.fq.gz

#84 stephlo76 opened 3 years ago
0
Kraken DB not available any more

#83 stephlo76 opened 3 years ago
0
Test fails: file missing

#82 stephlo76 opened 3 years ago
0
add -L option to raise cutoff to allow indel calling

#81 danrlu closed 3 years ago
2
vcf is misisng most INDELs

#80 danrlu closed 3 years ago
1
increase upper threshold of max mutations allowed

#79 danrlu closed 3 years ago
0
Add License

#78 batson closed 3 years ago
3
make tree output in pdf format

#77 danrlu closed 3 years ago
1
Add nf-core style custom configs

#76 olgabot opened 3 years ago
0
Allow running plain metagenomics (without MSSPE primers)

#75 jackkamm closed 3 years ago
1
Update default test.config to be ARTIC

#74 danrlu closed 3 years ago
0
Avoid +N insertions

#73 jackkamm opened 3 years ago
0
[meta] Pipeline and repo cleanup

#72 jackkamm opened 3 years ago
1
[minor] Better handling of skipping ERCC process

#71 jackkamm opened 3 years ago
2
Unit tests for ARTIC

#70 jackkamm closed 3 years ago
1
Make pipeline work when number of samples is 2 or less

#69 jackkamm closed 3 years ago
0
Error running pipeline when sample size is 2 or less

#68 nhatas closed 3 years ago
5
skip trimming primers

#67 nhatas opened 3 years ago
1
Add ability to use czbiohub_aws config

#66 olgabot opened 3 years ago
0
Fix/remove test_fasta_reads, test_single_end

#65 jackkamm opened 3 years ago
0
Change read filtering options

#64 jackkamm closed 4 years ago
2
exit with error message if reads not found

#63 samlhao opened 4 years ago
0
wrapper script to call secret to get weblogs url

#62 phoenixAja closed 2 years ago
0
Fix profiles

#61 samlhao closed 4 years ago
1
Documentation

#60 samlhao closed 4 years ago
1
add weblog scope to nextflow.config

#59 samlhao closed 4 years ago
0
Remove pileup minimum depth

#58 jackkamm closed 4 years ago
0
Add --save_filtered_reads option

#57 olgabot closed 4 years ago
1
Fix indel calling

#56 samlhao closed 3 years ago
1
add intrahost nucleotide diversity stat

#55 samlhao closed 3 years ago
0
add filtered_reads column to combined.stats.tsv

#54 samlhao closed 3 years ago
0
publish host-filtered reads

#53 samlhao closed 4 years ago
0
Single end fastqs

#52 jackkamm closed 3 years ago
1
Unpaired reads and bad test sample

#51 jackkamm opened 4 years ago
1
Speed up filtering step

#50 samlhao closed 3 years ago
6
add baseDir to test config

#49 samlhao closed 4 years ago
0
Rename call_consensus.nf to main.nf

#48 jackkamm closed 4 years ago
3
Test data configs are not portable

#47 evanfloden closed 4 years ago
0
exit and print error if kraken2_db not set

#46 samlhao opened 4 years ago
2
visualization of read support for variants

#45 samlhao closed 3 years ago
0
Implement proper variant calling

#44 jackkamm closed 4 years ago
1
Add annotation step with VADR

#43 jackkamm closed 3 years ago
0
Updated test conf for host ref.

#42 neevor closed 4 years ago
0
Rename this repo

#41 jackkamm closed 4 years ago
1
Improved VCF files

#40 jackkamm closed 4 years ago
0
Use minimap2 to remove host reads.

#39 neevor closed 4 years ago
1
Automated reporting of newly assembled genomes

#38 batson closed 3 years ago
0
Bad dash

#37 batson closed 4 years ago
0