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Dev #2

Merged
merged 20 commits into from
Jan 24, 2024
Merged

Dev #2

merged 20 commits into from
Jan 24, 2024

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kubranarci
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current devs

@kubranarci
HDR estimation module is done
c9a5eb1
@kubranarci
beagle reference problem resolved
d1cfce6
@kubranarci
Hg37 (#1)
8318846 
* Add files via upload

* hg37 changes

* hg37 changes

* Delete modules/nf-core/bedtools/intersect directory

not needed

* Delete modules/nf-core/tabix/bgziptabix directory

not needed

* hg37 changes

* hg37 changes
@kubranarci
male corrections
6d07437
@kubranarci kubranarci self-assigned this Oct 24, 2023
@kubranarci
minor changes
8acac28
@kubranarci
fake control pipeline is functional (#6)
0fc1519
@kubranarci
SV input in samplesheet (#8)
48ddcef
@kubranarci
missing sv column
c35c268
@kubranarci
Delete subworkflows/local/breakpoints_segments.nf
28ccc8f
@kubranarci
Delete results37 directory
80e898b
@kubranarci
5 no control pipeline bug 3 (#11)
7ad5fb4 
* nocontrol workflow fixed

* Delete results37 directory
@kubranarci
changes implemented (#12)
9c84b4c
@kubranarci
document updated (#13)
9de89fc
@kubranarci
multi-sample ready (#19)
c17754d
@kubranarci
resources optimized (#20)
84b8baa
@kubranarci
small changes
4a81ce4
@kubranarci
14 create test dataset (#23)
f7f8a40 
* Delete seqc2_testdata_aceseq directory

* ACE-seq test dataset

* testdataset additions

* get beagle ref automatically

* annotations testdata

* testdata

* small changes

* beagle ref hg37 added to igenomes

* testdata is running hg19
@kubranarci kubranarci marked this pull request as draft January 23, 2024 10:19
@kubranarci
15 cicd tests (#24)
68acc55 
* Create main.yml

* files added

* singularity removed and args cleaned

* fix
@kubranarci
prettier and small fixes
61b1ed2
@kubranarci
delete some files
500dd5a
@kubranarci kubranarci requested a review from drewjbeh January 24, 2024 13:20
@kubranarci kubranarci marked this pull request as ready for review January 24, 2024 13:20
@kubranarci kubranarci merged commit 4019e4c into main Jan 24, 2024
4 checks passed
@kubranarci kubranarci removed the request for review from drewjbeh January 24, 2024 13:21
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