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nf-core
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ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Improve reporting
#657
d4straub
closed
1 year ago
1
Move conda check to script section
#656
d4straub
closed
1 year ago
2
Fix nextflow version 23.10.0 with QIIME2
#655
d4straub
closed
1 year ago
2
Nextflow version 23.10.0 is incompatible with QIIME2 (pipeline fails), solution: prepend 'NXF_VER=23.04.4' when running the pipeline
#654
bioinfogaby
closed
1 year ago
17
I didn't receive an email notification
#653
luozhy88
closed
1 year ago
3
Report shows wrong taxonomic classification stats for QIIME with UNITE
#652
d4straub
closed
1 year ago
3
Bump version to 2.8.0dev
#651
d4straub
closed
1 year ago
2
Requirement Exceeds Available Memory for CUTADAPT
#650
aqsakhalid03
closed
1 year ago
7
CUTADAPT Workflow error
#649
aqsakhalid03
closed
1 year ago
5
Release 2.7.0
#648
d4straub
closed
1 year ago
2
Prepare 2.7.0 release
#647
d4straub
closed
1 year ago
2
Update dependencies
#646
d4straub
closed
1 year ago
2
Update workflow overview figure & docs
#645
d4straub
closed
1 year ago
1
Update pipeline summary report
#644
d4straub
closed
1 year ago
1
Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp
#643
d4straub
closed
1 year ago
2
Merging template updates 2.10
#642
d4straub
closed
1 year ago
2
Continue analysis even when individual files fail the filtering threshold
#641
sminot
closed
1 year ago
5
Important! Template update for nf-core/tools v2.10
#640
nf-core-bot
closed
1 year ago
0
Add GTDB 214.1 for DADA2
#639
d4straub
closed
1 year ago
1
Catch error case where 0 reads pass filtering and params.ignore_failed_trimming = True
#638
sminot
closed
1 year ago
8
Add taxonomic classification with kraken2
#637
d4straub
closed
1 year ago
2
Adding gtdb release 214 & adding already downloaded database
#636
x-rv
closed
1 year ago
2
Broken link in README.md
#635
a4000
closed
1 year ago
2
A feature to remove taxa found in controls
#634
skose82
opened
1 year ago
5
disable GPU for UNIFRAC
#633
d4straub
closed
1 year ago
2
Add alpha diversity to sample count correlation to report
#632
d4straub
closed
1 year ago
2
Add vsearch uchime_denovo for chimera removal (or flagging)
#631
andand
opened
1 year ago
2
Fix filters with --input_fasta
#630
d4straub
closed
1 year ago
4
Fasta input isnt compatible with most filters
#629
d4straub
closed
1 year ago
2
Prevent rare error with sample sheet edge case
#628
d4straub
closed
1 year ago
2
Cutadapt failing due to renaming of files
#627
susheelbhanu
closed
1 year ago
8
RENAME_RAW_DATA_FILES - Process requirement exceeds available CPUs
#626
amalacrino
closed
1 year ago
2
Manuscript methods section and VSEARCH cluster to pipeline report
#625
d4straub
closed
1 year ago
2
fix typo in quick start command
#624
d4straub
closed
1 year ago
1
Error in command
#623
dixi06
closed
1 year ago
2
add VSEARCH cluster
#622
a4000
closed
1 year ago
1
Update nextflow_schema.json
#621
jtangrot
closed
1 year ago
1
Update multiqc methods
#620
d4straub
closed
1 year ago
2
add SBDI export and phyloseq output to summary report
#619
d4straub
closed
1 year ago
2
Add sintax support for all available databases
#618
jtangrot
opened
1 year ago
1
Check for SBDI compatibility for sintax
#617
jtangrot
closed
1 year ago
2
Use nf-validation on samplesheet
#616
d4straub
closed
1 year ago
3
Dev
#615
a4000
closed
1 year ago
2
Merging template updates 2.9
#614
d4straub
closed
1 year ago
1
Potential problem with demultiplexing and proposed solution
#613
a4000
opened
1 year ago
1
Proposal: Phyloseq R object creation at end of pipeline
#612
a4000
closed
1 year ago
7
Proposal: Seqkit stats when demultiplexing
#611
a4000
opened
1 year ago
2
Proposal: Lowest Common Ancestor (LCA) module for assigning taxonomy
#610
a4000
opened
1 year ago
2
Proposal: LULU ASV post-clustering curation
#609
a4000
closed
1 year ago
9
Proposal: Blastn as an alternative classifier
#608
a4000
opened
1 year ago
6
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