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feat: update multiqc to 1.22.3 #1441

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merged 45 commits into from
Jun 26, 2024
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94f240d
changelog initial
mathiasbio Mar 7, 2024
9058d3d
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Apr 15, 2024
6bfa0b3
merge develop
mathiasbio Apr 15, 2024
711f0ae
add hardcoded sentieon path
mathiasbio Apr 30, 2024
15cc2ba
remove TNscope ML model and unused callers
mathiasbio May 14, 2024
451286a
fix bug
mathiasbio May 14, 2024
9124b00
update multiqc to 1.22.1
mathiasbio May 29, 2024
7bbfb9d
update version in docs
mathiasbio May 29, 2024
59ba636
removed sed command
mathiasbio May 29, 2024
aa2074b
changelog
mathiasbio May 29, 2024
c627d29
add separate multiqc container
mathiasbio May 30, 2024
7932570
remove multiqc from align sif
mathiasbio May 30, 2024
6f6334f
add build to actions
mathiasbio May 30, 2024
2dabf3c
add test script
mathiasbio May 30, 2024
62d76aa
update which container to use
mathiasbio May 30, 2024
b706a5b
temporary alignqc sif
mathiasbio May 30, 2024
a132407
return align sif name
mathiasbio May 30, 2024
f7947c7
attempting downgrade to 1.18 to fix somalier issue
mathiasbio May 31, 2024
858ebef
update multiqc to 1.22.2
mathiasbio Jun 3, 2024
c1514d9
go back to version 1.18
mathiasbio Jun 3, 2024
8188756
change collect qc metrics sample id parsing
mathiasbio Jun 3, 2024
50c2171
black
mathiasbio Jun 3, 2024
0bb287d
updated changelog
mathiasbio Jun 3, 2024
c217ec3
fix pytest
mathiasbio Jun 3, 2024
435abec
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Jun 3, 2024
dd8607c
Merge branch 'develop' into update_multiqc
mathiasbio Jun 3, 2024
445c967
update to 1.22.2
mathiasbio Jun 4, 2024
33bd896
return to 1.18
mathiasbio Jun 5, 2024
6f5b681
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Jun 25, 2024
43b5edf
Merge branch 'develop' into update_sentieon
mathiasbio Jun 25, 2024
a449de9
update multiqc container to v.1.22.3
mathiasbio Jun 25, 2024
38bc18d
merge conflicts
mathiasbio Jun 25, 2024
2c060e7
revert sentieon changes
mathiasbio Jun 25, 2024
27aa96c
lalala
mathiasbio Jun 25, 2024
4f20a73
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Jun 25, 2024
61e134a
fix conflict
mathiasbio Jun 25, 2024
48bb6eb
add doubleqoutes
mathiasbio Jun 25, 2024
bbb40c8
double qoute
mathiasbio Jun 25, 2024
f94a474
add test
mathiasbio Jun 26, 2024
6e439b4
black
mathiasbio Jun 26, 2024
3a196d2
code review
mathiasbio Jun 26, 2024
063d9a6
Update CHANGELOG.rst
mathiasbio Jun 26, 2024
02eccc8
modifying dockerfile
mathiasbio Jun 26, 2024
2cb3a93
Merge branch 'update_multiqc' of github.com:Clinical-Genomics/BALSAMI…
mathiasbio Jun 26, 2024
f222381
fix after codereview
mathiasbio Jun 26, 2024
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lalala
mathiasbio committed Jun 25, 2024
commit 27aa96c1491e6bf3208cf8c76ab7ff56e1cb636a
Original file line number Diff line number Diff line change
@@ -85,7 +85,7 @@ rule sentieon_TNscope:
pcr_model = params.common.pcr_model,
tumor_options = VARCALL_PARAMS["tnscope"]["tumor"],
normal_options = VARCALL_PARAMS["tnscope"]["normal"],
sentieon_ml_tnscope= config["SENTIEON_TNSCOPE"],
sentieon_ml_tnscope = config["SENTIEON_TNSCOPE"],
sentieon_exec = config["SENTIEON_EXEC"],
sentieon_lic = config["SENTIEON_LICENSE"],
case_name = config["analysis"]["case_id"]