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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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Add downsample: [int] to params
#38
crosenth
closed
3 years ago
1
Create parameter "bidirectional" for uNGS steps
#37
crosenth
closed
3 years ago
1
WIP: changes to accommodate universalNGS application
#36
mwohl
closed
3 years ago
1
singularity support
#35
nhoffman
closed
1 year ago
4
Update base r image used in Dockerfile to fix dependency issue
#34
mwohl
closed
3 years ago
0
Dependency issue when building docker image
#33
mwohl
closed
3 years ago
1
Fix breaking comment syntax in config -- change from # to //
#32
mwohl
closed
3 years ago
0
Unable to parse config error
#31
mwohl
closed
1 year ago
0
Why are there 2 requirements.txt files?
#30
crosenth
closed
1 year ago
3
Fix issue with zero-padding in sv names
#29
mwohl
closed
3 years ago
0
Provide NGS16S specific settings for dada2 as pipeline params
#28
dhoogest
closed
2 years ago
0
Replicate current NGS16S pipeline settings for barcodecop, dada2
#27
dhoogest
closed
2 years ago
2
cmsearch will not report low quality sequence searches
#26
crosenth
closed
3 years ago
5
cmalign phase omitting some seqs from output
#25
dhoogest
closed
1 year ago
3
extend manifest KEEP_COLS to include NGS16S input metadata cols
#24
dhoogest
closed
3 years ago
0
Extend manifest.KEEP_COLS list or otherwise facilitate columns from input manifest propagation to output sample_info.csv
#23
dhoogest
closed
3 years ago
0
SV padding irregularities during eval of clinical NGS16S data
#22
dhoogest
closed
1 year ago
5
Extend test-single set to include readfiles with unmerged seqs of interest, alternate sample-info for NGS16S
#21
dhoogest
closed
3 years ago
0
write the input fastq_files.txt to output
#20
dhoogest
closed
3 years ago
2
Add fastq_list.txt file specified specified in params.json to pipeline output
#19
dhoogest
closed
3 years ago
3
numeric sv labels for each sample should be assigned in order of descending weight
#18
dhoogest
closed
2 years ago
6
Incorporate logic from chim_ints.R script into dada2-nf pipeline
#17
dhoogest
opened
3 years ago
3
Updating covariance model from Rfam database
#16
crosenth
closed
3 years ago
0
Labmed cloud integration
#15
crosenth
closed
3 years ago
1
switching from cmalign to cmsearch
#14
crosenth
closed
3 years ago
3
Replace cmalign 16s filtering step with cmsearch
#13
crosenth
closed
3 years ago
1
add test data for sample with known unmerged reads of interest
#12
dhoogest
closed
3 years ago
2
Include unmerged 16S SVs in pipeline output
#11
dhoogest
closed
2 years ago
3
Allow error model to be built from all reads
#10
tholland
closed
1 year ago
0
Make rds file accessible in output
#9
tholland
closed
4 years ago
0
Heuristics for filtering and trimming parameters
#8
wbazant
opened
4 years ago
2
Accommodate specimens with no index reads
#7
crosenth
closed
4 years ago
0
Make Index read input optional
#6
crosenth
closed
4 years ago
0
Referencing git hash in nextflow
#5
nkrumm
opened
4 years ago
0
Update queue in uw_batch profile to molmicro-queue
#4
nkrumm
closed
4 years ago
0
Update for batchman
#3
nkrumm
closed
4 years ago
1
001 per sample dereplication
#2
nhoffman
closed
4 years ago
0
per-sample dereplication
#1
nhoffman
closed
4 years ago
0
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