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stenglein-lab
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tick_surveillance
Bioinformatics pipeline for analysis of amplicon sequencing of tick-associated microbes
Apache License 2.0
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Issue with conda installation of cutadapt
#101
stenglein-lab
opened
2 weeks ago
0
dada2 filtering/trimming output table has shifted columns when some samples have 0 reads
#100
stenglein-lab
opened
1 month ago
0
Make a parameter to set a min cutoff for calling Acceptable_DNA
#99
stenglein-lab
closed
2 weeks ago
1
Dev
#98
stenglein-lab
closed
1 month ago
0
Trimmed_fastq output directory not being populated?
#97
stenglein-lab
closed
1 month ago
1
FASTQC reports in results directory
#96
stenglein-lab
closed
1 month ago
0
Switch to DSL2
#95
stenglein-lab
closed
1 month ago
0
explore use of core_nt database
#94
stenglein-lab
opened
2 months ago
0
Surveillance target behavior with respect to species-level assignments
#93
stenglein-lab
opened
5 months ago
0
Update R package (rocker tidyverse image)
#92
stenglein-lab
closed
1 month ago
1
Changing "Testing Results" --> "TestingResults" tab in main output workbook
#91
stenglein-lab
closed
6 months ago
1
Add the ability to use taxonomizr R package
#90
stenglein-lab
opened
7 months ago
0
Positive / negative calls not being made for A1-A96
#89
stenglein-lab
closed
8 months ago
1
Switch to modular conda definitions instead of all-in-one conda environment
#88
stenglein-lab
closed
1 month ago
0
Don't setup singularity python environment when using conda
#87
stenglein-lab
closed
1 month ago
0
Would it be useful to create nf-core-style meta.yml files for local modules?
#86
stenglein-lab
opened
1 year ago
0
Merge in recent changes to DSL2 branch
#85
stenglein-lab
closed
1 year ago
0
Merge in recent changes to dev to close #14 and #81 on dsl1 branch
#84
stenglein-lab
closed
1 year ago
0
Make DSL2 version the main / default branch?
#83
stenglein-lab
closed
1 month ago
0
At some point, will need to change singularity to apptainer?
#82
stenglein-lab
opened
1 year ago
0
all_data_and_medadata columns shifted
#81
stenglein-lab
closed
1 year ago
6
DSL2 multiQC missing content
#80
stenglein-lab
closed
1 month ago
0
remove unneeded input dir from repo
#79
stenglein-lab
closed
1 year ago
1
Make sure helpful warning/error messages if required inputs missing
#78
stenglein-lab
closed
1 month ago
1
figure out how to make python module installation more reproducible
#77
stenglein-lab
closed
1 year ago
2
python venv install issue
#76
stenglein-lab
closed
1 year ago
3
issue with R package dependencies when running with conda
#75
stenglein-lab
closed
1 month ago
2
Remote BLAST of unassigned sequences no longer works
#74
stenglein-lab
closed
1 year ago
0
Remove cpus and memory from executor block in sge.config
#73
stenglein-lab
closed
1 month ago
1
Delete no-longer needed metadata files in input directory
#72
stenglein-lab
closed
11 months ago
0
Merge recent work on dev into main
#71
stenglein-lab
closed
1 year ago
0
Rickettsia not detected
#70
stenglein-lab
closed
1 year ago
1
add refseq fastas to results folder
#69
stenglein-lab
closed
1 year ago
1
Update README and other documents in the containers/singularity directory
#68
stenglein-lab
closed
1 year ago
0
In the worksheet tab formerly known as surveillance, there is an extra formatted column at the right end.
#67
stenglein-lab
closed
1 year ago
0
Need to make sure input file paths handled as path or file objects
#66
stenglein-lab
closed
1 year ago
0
Change name of surveillance tab in sequencing report file to "Testing Results"
#65
stenglein-lab
closed
1 year ago
0
Date columns in metadata get converted to epoch time during xls output
#64
stenglein-lab
closed
1 year ago
2
Why does dada2 re-run even when it doesn't have to?
#63
stenglein-lab
closed
1 year ago
3
Merge recent changes into main. These changes collectively address and close #2, #14, #55, #56, #57, #58, #61.
#62
stenglein-lab
closed
1 year ago
0
surveillance report generation doesn't work as expected if Index column not defined as a surveillance column
#61
stenglein-lab
closed
1 year ago
0
Consider switching trim_primer_seqs to process_high
#60
stenglein-lab
closed
1 year ago
2
More csv output
#59
stenglein-lab
closed
1 year ago
0
surveillance worksheet not populated when run from pipeline
#58
stenglein-lab
closed
1 year ago
0
Don't create refseq fasta files in refseq directory - create in work directory
#57
stenglein-lab
closed
1 year ago
0
Fix primer names in targets.tsv and primers.tsv, which use inconsistent names
#56
stenglein-lab
closed
1 year ago
1
Make sure local blast databases are available even if outside Singularity's default mounts
#55
stenglein-lab
closed
1 year ago
0
Merge in changes to enable pipeline to run in CDC HPC environment
#54
stenglein-lab
closed
1 year ago
0
Merge recent changes from main into dev to keep dev up to date
#53
stenglein-lab
closed
1 year ago
0
Phylo dev
#52
stenglein-lab
closed
1 year ago
0
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