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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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DSL2: add reference masking for PMDtools
#1029
scarlhoff
closed
6 months ago
0
new subworkflow: DSL2 sex determination
#1028
jbv2
closed
3 months ago
0
DSL1 Pipeline completed with errors / bug in test
#1027
0victormh0
closed
5 months ago
17
DSL2: Allow changing parameters for BWA mem.
#1026
TCLamnidis
opened
8 months ago
0
Important! Template update for nf-core/tools v2.10
#1025
nf-core-bot
closed
9 months ago
1
DSL1: multiqc_general_stats.txt is not generated when the table is a beeswarm plot in the report.
#1024
TCLamnidis
closed
8 months ago
0
Dsl2 add sharding of fastqs before alignment
#1023
shyama-mama
closed
7 months ago
8
DSL2: Add mapDamage as an alternative to DamageProfiler
#1022
TCLamnidis
closed
3 months ago
0
Dsl1 2.5.0
#1021
TCLamnidis
closed
8 months ago
10
DSL1: Add possibility to use MapDamage for damage estimation
#1020
TCLamnidis
closed
8 months ago
0
DSL2: metagenomics
#1019
ilight1542
opened
11 months ago
12
DSL2: Pull input files from reference sheet columns
#1018
scarlhoff
closed
8 months ago
1
DSL1: Input file name collision when merging two already merged BAMs in `additional_library_merge` step.
#1017
TCLamnidis
closed
8 months ago
3
DSL2: genotyping
#1016
TCLamnidis
closed
3 months ago
14
DSL2: Add HapCON?
#1015
TCLamnidis
opened
11 months ago
0
Adding new qualimap
#1014
jbv2
closed
10 months ago
9
DSL2: replaces input_check with fromSamplesheet (nf-validation)
#1013
jfy133
closed
1 month ago
9
DSL2: replace samplesheet check with nf-validation!
#1012
jfy133
closed
3 months ago
3
Adding new qualimap
#1011
jbv2
closed
11 months ago
0
DSL2: Input BAM2FASTQ
#1010
jfy133
closed
3 months ago
4
Dsl2 meta mapping function
#1009
TCLamnidis
closed
11 months ago
2
Important! Template update for nf-core/tools v2.9
#1008
nf-core-bot
closed
1 year ago
1
DSL2: adapt test_humanbam profile
#1007
scarlhoff
closed
1 year ago
1
DSL2: Add sharding of FASTQs before alignment
#1006
shyama-mama
closed
7 months ago
0
adding bedtool coverage from eager 2
#1005
shyama-mama
closed
11 months ago
3
DSL2: fixing print nuclear contamination output
#1004
scarlhoff
closed
1 year ago
1
DSL2: fix print contamination output
#1003
scarlhoff
closed
1 year ago
1
DSL2: Add bedtools coverage
#1002
jfy133
closed
8 months ago
4
DSL2: Add to MultiQC support for coverage_across_reference.txt file
#1001
jfy133
opened
1 year ago
0
DSL2: print contamination module only prints one sample
#1000
scarlhoff
closed
11 months ago
0
DSL2: BAM to FastQ conversion. Ensure that lane info is kept.
#999
TCLamnidis
closed
2 days ago
1
DSL2: Qualimap
#998
jbv2
closed
11 months ago
2
DSL2: Add qualimap module
#997
jbv2
closed
8 months ago
0
DSL2: Tweaks to modules config to avoid configuration overwrites
#996
TCLamnidis
closed
1 year ago
3
DSL2: Print Nuclear Contamination JSON `N/A` value
#995
TCLamnidis
opened
1 year ago
2
DSL2: Ensure to document input run BAMs will _not_ be merged with FASTQ libraries even if same name
#994
jfy133
opened
1 year ago
2
DSL2: current FASTQ_ALIGN subworkflow does not keep correct read + index combination
#993
jfy133
closed
4 months ago
1
Hello! I'm not shure this is the right place to ask for help but I'm having problems when running MaltExtract, I get this error: Error in image.default(x = 1:ncol(red.res), y = 1:nrow(red.res), z = t(red.res), : increasing 'x' and 'y' values expected Calls: image -> image.default
#991
crisamor
closed
1 year ago
2
Outputs of Damage Manipulation should include `${meta.reference}`
#990
TCLamnidis
closed
5 months ago
1
DSL2: PMDTools for estimation vs manipulation of damage
#989
TCLamnidis
opened
1 year ago
0
DSL2: Add popgen input files to reference sheet
#988
scarlhoff
closed
8 months ago
0
DSL2: Add input BAM BAM2FASTQ conversion support for remapping
#987
jfy133
closed
2 days ago
0
DSL2: Add test profile that forces ALL the possible merging steps for FastQ and BAM inputs, to ensure no file name collisions happen.
#986
TCLamnidis
opened
1 year ago
0
DSL2: Add `lane` attribute to BAM inputs
#985
TCLamnidis
opened
1 year ago
0
2.4.7 Patch
#984
jfy133
closed
1 year ago
2
MultiQC error
#983
MinLuke
closed
1 year ago
5
DSL2: Update input check
#982
TCLamnidis
closed
1 year ago
1
Fix CI tests
#981
jfy133
closed
1 year ago
1
Update all modules to include new container structure
#980
jfy133
closed
1 year ago
1
DSL2: ensure versions.yml aren't published
#979
scarlhoff
opened
1 year ago
1
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