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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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Add lane merging output directory to output documentation.
#1079
TCLamnidis
closed
6 days ago
0
Bump BWA version
#1078
jch-13
closed
1 week ago
1
DSL2: Genotyping on multiple snp sets in one run?
#1077
TCLamnidis
opened
1 week ago
1
DSL2: Starting subworkflow for circularmapper
#1076
jbv2
opened
2 weeks ago
1
Fix issue with MQC not displaying post-ar trimming FastQC results
#1075
jfy133
closed
6 days ago
4
Fix issue with MQC not displaying post-ar trimming FastQC results
#1074
jfy133
closed
3 weeks ago
3
MultiQC doesn't display post artrimming FASTQC results
#1073
jfy133
closed
6 days ago
0
DSL2: Add mapAD
#1072
jch-13
opened
1 month ago
1
DSL2: Schema and documentation consistency
#1071
scarlhoff
closed
6 days ago
1
DSL2: Add 'output' documention for mtnucratio
#1070
scarlhoff
opened
1 month ago
0
DSL2: Add MultiVCFAnalyzer
#1069
aidaanva
opened
1 month ago
0
Important! Template update for nf-core/tools v2.14.1
#1068
nf-core-bot
closed
1 month ago
1
Important! Template update for nf-core/tools v2.14.0
#1067
nf-core-bot
closed
1 month ago
1
DSL2: Ensure modules config consistency: all modules have an `ext.prefix` and `publishDir` attribute, and follow conventions.
#1066
TCLamnidis
opened
2 months ago
0
Use Sample-level merged BAMs for sample-level statistics
#1065
TCLamnidis
opened
2 months ago
1
add ext.prefix
#1064
TCLamnidis
closed
2 months ago
1
Add nf-test
#1063
jfy133
opened
2 months ago
3
added config for malt testing
#1062
ilight1542
closed
2 months ago
2
Add kraken2 test-profile, add UNTAR module
#1061
merszym
closed
2 months ago
1
DSL2: Convert input BAM
#1060
TCLamnidis
closed
1 month ago
4
CRAM output
#1059
TCLamnidis
opened
3 months ago
1
Add angsd gl
#1058
TCLamnidis
closed
3 months ago
1
Update rgs
#1057
TCLamnidis
closed
3 months ago
1
Important! Template update for nf-core/tools v2.13.1
#1056
nf-core-bot
closed
3 months ago
1
Fix description of mt/n ratio in docs
#1055
TCLamnidis
opened
4 months ago
0
Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed
#1054
TCLamnidis
opened
4 months ago
0
Important! Template update for nf-core/tools v2.13
#1053
nf-core-bot
closed
4 months ago
0
Patch 2.5.1
#1052
TCLamnidis
closed
4 months ago
4
Input BAM files overwritten and emptied when using same filename as ID
#1051
PCQuilis
closed
4 months ago
1
DSL2: metagenomics testing for malt fixes
#1050
ilight1542
closed
3 months ago
1
Update eager version on figures to 2.5
#1049
TCLamnidis
closed
4 months ago
1
Deprecate vcf2genome `--vcf2genome_outfile` parameter
#1048
TCLamnidis
closed
4 months ago
1
DSL1: Update multiqc clean_names to clean new names added in 2.5.0
#1047
TCLamnidis
closed
4 months ago
1
DSL2: Add rg info to BWA_MEM
#1046
TCLamnidis
closed
4 months ago
2
Dsl2 map damage
#1045
scarlhoff
closed
4 months ago
1
DSL2: add test including bedtools BED file for feature stats
#1044
jfy133
closed
5 months ago
1
DSL2: library merge
#1043
TCLamnidis
closed
5 months ago
4
DSL2: Add `LB:` to RG tags for all mappers
#1042
TCLamnidis
closed
1 month ago
0
Important! Template update for nf-core/tools v2.12
#1041
nf-core-bot
closed
5 months ago
2
DSL2: 'single_end' and 'id_index' not present in meta of BAM input
#1040
TCLamnidis
closed
3 months ago
3
DSL2: Add library merge step after damage_manipulation
#1039
TCLamnidis
closed
3 months ago
1
Important! Template update for nf-core/tools v2.11
#1038
nf-core-bot
closed
5 months ago
3
bedtools coverage fails when gff file and genome file are not sorted the same way
#1037
IdoBar
closed
4 months ago
1
Fix bedtools coverage in DSL1
#1036
IdoBar
closed
4 months ago
4
Dsl2 sex determination
#1035
jbv2
closed
3 months ago
1
Dsl2 bam2fq
#1034
TCLamnidis
closed
7 months ago
0
DSL2: add circularmapper module
#1033
shyama-mama
opened
8 months ago
3
DSL1: Release 2.5.0 - Bopfingen
#1032
TCLamnidis
closed
8 months ago
1
DSL1: No fasta indexing when using bowtie2.
#1031
TCLamnidis
closed
8 months ago
0
DSL2: add reference masking for PMDtools
#1030
scarlhoff
closed
6 months ago
1
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