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nf-core
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eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Patch: increase mean/median X coverage significance values
#932
jfy133
closed
1 year ago
3
Patch release dependency updates
#931
jfy133
closed
1 year ago
1
Re-add picard createorreplacereadgroups for MultiVCFanalyzer
#930
jfy133
closed
1 year ago
5
Try fix for damageprofiler sometimes needing a fai file
#929
jfy133
closed
1 year ago
2
Change read groups for genotyping when using MultiVCFAnalyzer
#928
aidaanva
closed
1 year ago
1
DSL2: Start adding fastp/adapterremoval
#927
jfy133
closed
1 year ago
5
DSL2: single-genome indexing
#926
jfy133
closed
1 year ago
3
New module: calmd
#925
JackCurragh
closed
1 year ago
4
DSL2: pop-gen
#924
jfy133
opened
1 year ago
0
DSL2: metagenomics
#923
jfy133
opened
1 year ago
6
DSL2: stats
#922
jfy133
opened
1 year ago
1
DSL2: preprocessing and mapping
#921
jfy133
opened
1 year ago
2
Important! Template update for nf-core/tools v2.6
#920
nf-core-bot
closed
1 year ago
1
Move eager3 development branch into dev
#919
jfy133
closed
1 year ago
1
Dev notes: eager3 don't forget list
#918
jfy133
opened
1 year ago
0
Mitochondrial and Ych haplotype callers
#917
SalWas1
opened
1 year ago
7
Important! Template update for nf-core/tools v2.5.1
#916
nf-core-bot
closed
1 year ago
1
Important! Template update for nf-core/tools v2.5
#915
nf-core-bot
closed
1 year ago
1
Fixed TSV input documentation
#914
aidaanva
closed
1 year ago
2
Endorspy license change
#913
aidaanva
closed
2 years ago
2
dev version bump
#912
TCLamnidis
closed
2 years ago
1
Patch release 2.4.5
#911
jfy133
closed
2 years ago
1
Linting fixes
#910
jfy133
closed
2 years ago
4
Pileupcaller paths fix
#909
TCLamnidis
closed
2 years ago
2
Minor update tube update
#908
jfy133
closed
2 years ago
3
Bump MultiQC so we get proper AR2 plots
#907
jfy133
closed
2 years ago
2
Resume after bwa aln not working
#906
jcgrenier
closed
2 years ago
8
Speed and memory optimization of `extract_map_reads.py`
#905
maxibor
closed
2 years ago
5
Mapped reads as input to metagenomic screening
#904
ilight1542
closed
1 year ago
2
Defaults fix
#903
jfy133
closed
2 years ago
2
Endorspy resume fix
#902
jfy133
closed
2 years ago
6
Add .gitpod.yml for remote working
#901
jfy133
closed
2 years ago
2
Fix circulargenerator assuming .fasta extension
#900
jfy133
closed
2 years ago
2
Circular generator crashes on bwa index when input fasta file does not end in .fasta
#899
scarlhoff
closed
2 years ago
3
Kraken2 empty fastq resulting in no output file fix
#898
jfy133
closed
2 years ago
4
Kraken breaks with missing output if 0 sequences
#897
alexandregilardet
closed
2 years ago
3
Output docs improvements
#896
jfy133
closed
2 years ago
3
Typo in output documentation and output documentation reporting in pipeline summary
#895
RodrigoBarquera
closed
2 years ago
1
container creation failed error
#894
hmedwards
closed
2 years ago
15
Possibility non-initial merge BAMs not sent to downstream bamtrim etc. steps?
#893
jfy133
closed
2 years ago
2
Remove deprecated params from benchmarking profiles
#892
jfy133
closed
2 years ago
2
Clarify clip_readlength help text for what is considered ultra-short …
#891
jfy133
closed
2 years ago
2
Patch getsoftwareversions java tools
#890
jfy133
closed
2 years ago
7
Update test configs
#889
TCLamnidis
closed
2 years ago
0
Channel mixup before `hostremoval_input_fastq` process
#888
maxibor
closed
2 years ago
1
Clarify "very short reads" in helptext of `clip_readlength`
#887
TCLamnidis
closed
2 years ago
0
Important! Template update for nf-core/tools v2.4
#886
nf-core-bot
closed
2 years ago
1
`get_software_versions` failing because of missing version files.
#885
maxibor
closed
2 years ago
2
Operator `into` has been deprecated -- it's not available in DSL2 syntax
#884
hypotheses
closed
2 years ago
2
Fastqc thread fix
#883
jfy133
closed
2 years ago
3
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