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Zymo-Research
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aladdin-shotgun
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updates for 0.0.4
#69
zxl124
closed
11 months ago
0
rebranding to aladdin
#68
zxl124
closed
11 months ago
0
Changes to the general stats table in the report
#67
zxl124
closed
11 months ago
0
consolidate params, update descriptions
#66
zxl124
closed
12 months ago
0
Ignore samples that failed sourmash steps
#65
zxl124
closed
1 year ago
0
Tie trimming length filter to kmer size; ignore failed samples
#64
zxl124
closed
1 year ago
0
Failure of One Sample May Crash Pipeline
#63
nsharp2
closed
1 year ago
1
New Reference Dataset Added
#62
nsharp2
closed
1 year ago
0
sample name cleaning; heatmap; database file updates
#61
zxl124
closed
1 year ago
0
Update how database files are staged in sourmash
#60
zxl124
closed
1 year ago
0
sourmash stage all database files, which causes too much I/O strain.
#59
zxl124
closed
1 year ago
0
rewrite heatmap code
#58
zxl124
closed
1 year ago
0
pipeline fails if sourmash is unable to find any matches
#57
nsharp2
closed
1 year ago
1
Change how fastqc names outputs and how MultiQC cleans sample names
#56
zxl124
closed
1 year ago
0
Change how fastqc names outputs and how MultiQC cleans sample names
#55
zxl124
closed
1 year ago
0
Pipeline does not check for read length against kmer size setting
#54
nsharp2
closed
1 year ago
0
MultiQC may fail with big sample groups
#53
nsharp2
opened
1 year ago
1
heatmap bugs
#52
zxl124
closed
1 year ago
0
Pipeline does not write FastQC results to MultiQC report if single end data is used
#51
nsharp2
closed
1 year ago
1
Reference dataset comparison and diversity code refactor
#50
zxl124
closed
1 year ago
0
Update how beta diversity PCoA plots are generated
#49
zxl124
closed
1 year ago
0
Compare with reference datasets
#48
zxl124
closed
1 year ago
0
Beta diversity plotting needs to be rewritten
#47
nsharp2
closed
1 year ago
0
Filter sample metadata for diversity analysis
#46
zxl124
closed
1 year ago
0
Groups without replicates causing bugs in diversity analysis
#45
zxl124
closed
1 year ago
0
Option to compare reference database diversity to sample diversity
#44
nsharp2
closed
1 year ago
0
zliu Issue30
#43
nsharp2
closed
1 year ago
0
Fix composition barplot bugs
#42
zxl124
closed
1 year ago
0
Composition barplot grouping function in report does not work as intended
#41
zxl124
closed
1 year ago
0
Issue 37: Heatmap errors when a group has no replicates
#40
nsharp2
closed
1 year ago
0
MultiQC Report Cleaned Up
#39
nsharp2
closed
1 year ago
0
Merge changes related to sourmash for testing
#38
zxl124
closed
1 year ago
0
heatmap step errors when there is a sample without replicates
#37
zxl124
closed
1 year ago
0
Clean up report summary and reorder sections
#36
zxl124
closed
1 year ago
0
Pipeline chops off "_1" from sample name
#35
zxl124
closed
1 year ago
0
Clean up report general stats table
#34
zxl124
closed
11 months ago
0
Make pipeline Aladdin compatible
#33
zxl124
closed
1 year ago
0
Qiime alphararefaction takes too long
#32
zxl124
opened
1 year ago
0
Host removal should use the genome index that come with the pipeline
#31
zxl124
opened
1 year ago
0
Revise how data are imported into Qiime
#30
zxl124
closed
1 year ago
0
khmer process added to profiling.nf
#29
nsharp2
closed
1 year ago
0
improperly placed sourmash variable removed
#28
nsharp2
closed
1 year ago
0
Move qiime code to a subworkflow
#27
nsharp2
closed
1 year ago
1
Clean up report
#26
zxl124
closed
1 year ago
0
Make the pipeline compatible with Aladdin
#25
zxl124
closed
11 months ago
0
convert database file into config
#24
zxl124
closed
1 year ago
0
pipeline now uses absolute counts to generate qiime barplot
#23
zxl124
closed
1 year ago
0
add khmer trim-low-abund
#22
zxl124
closed
1 year ago
0
add sourmash
#21
zxl124
closed
1 year ago
0
sample counts now summed across duplicate clade names
#20
nsharp2
closed
1 year ago
0
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