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feat: add MuSE as new somatic variant caller #1744

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f500911
feat: install muse
famosab Dec 4, 2024
b5421ac
feat: add muse variant calling sbwf
famosab Dec 4, 2024
d1940b2
feat: add muse
famosab Dec 4, 2024
66bc786
feat: add muse to schema
famosab Dec 4, 2024
a5ec509
feat: convert to bam
famosab Dec 4, 2024
2c1b86a
feat: add fai as input
famosab Dec 4, 2024
d404105
add conf
famosab Dec 5, 2024
23cc481
Update nextflow_schema.json
famosab Dec 5, 2024
8c722e6
fix: swap to cram_tumor and cram_normal
famosab Dec 5, 2024
7f7dfb6
feat: add to changelog and docs
famosab Dec 5, 2024
4e8ce41
feat: add to README
famosab Dec 5, 2024
0747d4c
feat: add muse to output
famosab Dec 5, 2024
e5e1358
feat: add muse to output
famosab Dec 5, 2024
92673c6
fix: changelog and citations
famosab Dec 5, 2024
4df5c16
fix: update prefix
famosab Dec 5, 2024
13a0521
feat: add test file for muse
famosab Dec 5, 2024
0375350
fix: prettier
famosab Dec 5, 2024
59dde7b
feat: add to pytest
famosab Dec 5, 2024
c4b2725
Merge branch 'dev' into muse
famosab Jan 7, 2025
c09d553
Merge branch 'nf-core:master' into muse
famosab Jan 7, 2025
3918b9c
Merge branch 'dev' into muse
famosab Feb 17, 2025
73db049
first steps to nf-test
famosab Feb 17, 2025
fdda799
expand nf-test
famosab Feb 17, 2025
a818507
remove pytest
famosab Feb 17, 2025
272c4e0
Update tests/config/pytesttags.yml
famosab Feb 17, 2025
c53ec09
remove trailing whitespace
famosab Feb 17, 2025
4ec7eb7
update muse modules with version fix
famosab Feb 18, 2025
1949b1e
Merge branch 'dev' into muse
famosab Feb 18, 2025
af604d5
updare snap
famosab Feb 18, 2025
ab4517b
remove counts from nft and update snap
famosab Feb 19, 2025
f181a7b
revert changes to nftignore
famosab Feb 20, 2025
df9bcc7
expand conf and update snap
famosab Feb 24, 2025
380551b
alphabetical ordering
famosab Feb 24, 2025
ceac08b
correct docs and bring into alphabetical order
famosab Feb 24, 2025
405943c
correct docs and bring into alphabetical order
famosab Feb 24, 2025
bb946ba
correct docs and bring into alphabetical order
famosab Feb 24, 2025
0f98500
Merge branch 'dev' into muse
famosab Feb 25, 2025
cedd3d4
Merge branch 'dev' into muse
famosab Feb 27, 2025
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22 changes: 22 additions & 0 deletions conf/modules/muse.config
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available keys to override module options:
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
ext.when = When to run the module.
----------------------------------------------------------------------------------------
*/

// MUSE

process {

withName: 'MUSE_SUMP' {
ext.args = { params.wes ? '-E' : '-G' }
}

}
2 changes: 1 addition & 1 deletion conf/test_full.config
Original file line number Diff line number Diff line change
@@ -18,7 +18,7 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'

// Other params
tools = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
tools = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff,muse'
split_fastq = 20000000
intervals = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
10 changes: 10 additions & 0 deletions modules.json
Original file line number Diff line number Diff line change
@@ -349,6 +349,16 @@
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"installed_by": ["modules"]
},
"muse/call": {
"branch": "master",
"git_sha": "219299d7fc22a55cd3a07c2122044e7ca24b815f",
"installed_by": ["modules"]
},
"muse/sump": {
"branch": "master",
"git_sha": "8e17f287034692420127d807c7631ae5ca4b9d0c",
"installed_by": ["modules"]
},
"ngscheckmate/ncm": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
5 changes: 5 additions & 0 deletions modules/nf-core/muse/call/environment.yml

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50 changes: 50 additions & 0 deletions modules/nf-core/muse/call/main.nf

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72 changes: 72 additions & 0 deletions modules/nf-core/muse/call/meta.yml

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72 changes: 72 additions & 0 deletions modules/nf-core/muse/call/tests/main.nf.test

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68 changes: 68 additions & 0 deletions modules/nf-core/muse/call/tests/main.nf.test.snap

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2 changes: 2 additions & 0 deletions modules/nf-core/muse/call/tests/tags.yml

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6 changes: 6 additions & 0 deletions modules/nf-core/muse/sump/environment.yml

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54 changes: 54 additions & 0 deletions modules/nf-core/muse/sump/main.nf

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