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nhoffman
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dada2-nf
A Nextflow pipeline for processing 16S rRNA sequences using dada2
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Preserve reads filtered out at dada2 filterAndTrim
#88
crosenth
closed
1 month ago
0
Preserve reads filtered out at dada2 filterAndTrim?
#87
marykstewart
opened
1 month ago
2
Update dada2 to latest version, 1.26
#86
mwohl
opened
3 months ago
0
Output map file(s) from raw reads -> r1,r2 -> merged
#85
crosenth
opened
7 months ago
0
Reinstate get_unmerged.R logic
#84
dhoogest
closed
7 months ago
11
Move params.output to the primary argument for publishDir
#83
sminot
closed
1 year ago
1
cirro integration
#82
nhoffman
opened
1 year ago
8
Cloud compatibility
#81
crosenth
closed
1 year ago
1
Please delete all stale and merged branches
#80
crosenth
closed
1 year ago
1
Test refactor
#79
crosenth
closed
1 year ago
0
Standardize input file(s)
#78
crosenth
closed
11 months ago
11
Dsl2 pipeline
#77
crosenth
closed
1 year ago
0
conditinalize in event that yld[si] is zero to avoid divide by zero err
#76
dhoogest
closed
1 year ago
2
an outright empty fastq errors in the plot_quality.R phase
#75
dhoogest
opened
1 year ago
3
modify iddef to 0 in vsearch combine_svs command
#74
dhoogest
closed
1 year ago
0
modify iddef strategy to 0 in combine_svs action
#73
dhoogest
closed
1 year ago
2
restore error model png to learn_errors output
#72
dhoogest
closed
1 year ago
1
Restore output of error_model plots
#71
dhoogest
closed
1 year ago
2
Need new CI/CD test case
#70
crosenth
closed
1 month ago
1
Create Mermaid diagram
#69
crosenth
opened
1 year ago
0
update changelog for version 1.19
#68
nhoffman
closed
1 year ago
1
Lots of updates
#67
crosenth
closed
1 year ago
0
Handle empty reads pre error model
#66
dhoogest
closed
1 year ago
1
Rework vsearch_svs process to ensure that clustering only occurrs within a sampleid rather than across all sequences
#65
dhoogest
closed
1 year ago
4
Binding sampleid with unmerged and chimera rds
#64
crosenth
closed
1 year ago
3
Orient reads after cutadapt
#63
crosenth
closed
1 year ago
3
sort df of unmerged seqs by desc abundance prior to generating output
#62
nhoffman
closed
1 year ago
0
Fix singularity container in nextflow.config
#61
dhoogest
closed
1 year ago
0
59 sort unmerged
#60
dhoogest
closed
1 year ago
1
Sort unmerged read fasta files in order of descending abundance
#59
dhoogest
closed
1 year ago
1
55 cutadapt
#58
dhoogest
closed
1 year ago
1
version bump docker base to rocker/r-ubuntu:22.04, install gridextra explicitly
#57
dhoogest
closed
1 year ago
1
Docker image build no longer successfully installing dada2
#56
dhoogest
closed
1 year ago
1
Incorporate cutadapt (or equivalent tool), add adaptor/primer seqs to parameter inputs
#55
dhoogest
closed
1 year ago
3
Support for ITS using vsearch alignments
#54
crosenth
closed
2 years ago
5
increasing trim to 19bp
#53
crosenth
closed
1 year ago
3
modify ungs dada2 params to incorporate ngs16s specific preferences
#52
dhoogest
closed
2 years ago
0
WIP: Handle null seqtab in get_chim_dropped.R
#51
dhoogest
closed
2 years ago
1
Actually add the chimera_dropped code
#50
dhoogest
closed
2 years ago
2
add script and process to extract unmerged seqs from the rds file
#49
dhoogest
closed
2 years ago
1
uncomment dada_get_unmerged, fix typo in params-ngs16s
#48
dhoogest
closed
2 years ago
1
Uncomment dada_get_unmerged process
#47
dhoogest
closed
2 years ago
0
Force dsl1 from config
#46
dhoogest
closed
2 years ago
2
add var barcodecop_head_cmd and append to barcodecop processes
#45
dhoogest
closed
2 years ago
3
'downsample' argument in params does not downsample reads from barcodecop onward
#44
dhoogest
closed
2 years ago
3
handle scenario where there are no merged seqs for a sample
#43
dhoogest
closed
2 years ago
1
specify name of work dir in params or via command line
#42
nhoffman
closed
1 month ago
1
add check.names=FALSE arg to read.csv to prevent 'X' escaping of 16S cols
#41
dhoogest
closed
2 years ago
1
Column name difference in counts.csv following upgrade in dada2 R dependencies
#40
dhoogest
closed
2 years ago
1
Add process to run get_unmerged
#39
dhoogest
closed
2 years ago
2
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