Swap sentieon/tnhaplotypecaller2 and tnscope to nf-test#8187

Merged

SPPearce merged 97 commits intomasterfrom

sention_tnhaplotyper2_nftest

Apr 18, 2025

Commits on Apr 1, 2025

Initial conversion, needs snapshots generating
SPPearce
committed

Commits on Apr 8, 2025

Add tnscope
SPPearce
committed

Commits on Apr 14, 2025

Update version for updateblastdb (#8181)
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Change FastQC memory parameter from float to int (#8180)

Schmytzi
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updated bandage image to latest version (#8185)

saramonzon
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portcullis/full: accommodate more outputs (#8166)

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update freyja module to latest version (#8184)

saramonzon
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Update bcftools (#8182)

saramonzon
and
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updated artic to latest version (#8186)

saramonzon
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Add functionality for `--unknown-slide` in `spaceranger/count` (#7233)

committed
Add threads parameter for all seqkit modules missing (#8192)

jfy133
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Support formula in `abundance_differential_filter` and associated modules (#8171)

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Update shinyngs modules (#8194)

pinin4fjords
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add module integronfinder (#8131)

authored and
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add gpu snapshot updater action (#8183)

mashehu
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Update dependency python to 3.13 (#8189)

renovate[bot]
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committed
Mindagap stub and test updates (#8200)

kbestak
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committed
fixed bug in bandage/image module, wrong versions.yml outputted (#8196)

saramonzon
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committed
fix formatting in sylphtax/taxprof (#8202)

authored and
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run update snapshot on gpu runners (#8201)

mashehu
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committed
add nf-test and stub to svtk/standardize (#7768)

kubranarci
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committed
fix typo in gpu-snapshot updater (#8204)

mashehu
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committed
update vep to 113.4 and redo conda tests (#8205)

nvnieuwk
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committed
Fix one more typo (#8207)

mashehu
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committed
change MUSE_SUMP to high memory module (#8212)

famosab
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committed
Update tj-actions/changed-files digest to 6cb76d0 (#8217)

renovate[bot]
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committed
Fix: PoolSNP: Update input tuple; cleanup stub (#8218)

abhilesh
authored and
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committed
Fix to rnaseq preprocessing linting fix (#8221)

pinin4fjords
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committed
Update modkit and porechop modules (#8223)

authored and
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Metaspace download (#8145)

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Update vrhyme modules, including nf-test (#8163)
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nf-test migration: cellrangerarc/count (#8008)

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Add sylphtax/merge and update taxprof to version 1.2 (#8228)

sofstam
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Clair3 (#7838)

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update to doubled runner resources (#8233)

mashehu
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committed
GTDBTK_CLASSIFYWF database improvement (#8220)

committed
handle filtered out modules and subworkflow files in the linting step correctly (#8235)

mashehu
authored and
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committed
fix linting check to run on files, not general changes (#8240)

mashehu
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always commit changes when run gpu-snapshot bot runs succesfully (#8237)

mashehu
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Plink2 hwe (#8227)

committed
migrate nf-test: survivor-filter (#8229)

committed
ragtag/scaffold and ragtag/patch modules and tests (#8198)

authored and
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Nf-test migration survivor/simsv (#8251)

kubranarci
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Stecfinder nftest (#8243)
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Fix mutect tests (#8242)

famosab
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nf-test migration: plink/indeppairwise (#8133)

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Uncomment logging. (#8248)

nschan
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Swap shigeifinder to nf-test (#8245)
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Migrate `cellrangerarc/mkref`to nf-test (#8219)

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Plink2 filter (#8247)

jodennehy
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Use modules_testdata_base_path (#8259)

maxulysse
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nf-test + stub: svtk/rdtest2vcf (#8258)

kubranarci
and
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dragmap hashtable - snapshot versions (#8261)

maxulysse
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Add gatk4/modelsegments (#8234)

lbeltrame
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Update GTDB-TK: Update container version and fix a couple of error sources [do not merge - waiting on local test] (#8255)

prototaxites
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Add custom adapters list as input argument (#8262)

sofstam
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Update GitHub Actions (#8253)

renovate[bot]
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Migrate `GENOTYPHI_PARSE` to nf-test (#8265)

LouisLeNezet
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committed
Fix prettier porechop meta (#8266)

sofstam
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committed
Fix errant bash comment in gtdbtk/classifywf (#8267)

prototaxites
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Downgrade dragmap to the previous functionning version (#8263)

maxulysse
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new module: fusioncatcher build (#8268)

nvnieuwk
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new module: fusioncatcher/fusioncatcher (#8271)

nvnieuwk
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Deprecate `FCS_FCSGX` (#8269)

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Migrate `gem2/gem2bedmappability` to nf-test (#8275)

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Migrate `gem2/gemmappability` to nf-test (#8278)

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Migrate `genescopefk` to nf-test (#8277)

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gatk4spark - better assertion and stub tests (#8274)

maxulysse
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Links (#8260)

nschan
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Migrate `damageprofiler` to nf-test (#8282)

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Bump genmod to 3.10 (#8281)

fellen31
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remove plink2 hwe (#8280)

jodennehy
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Merge remote-tracking branch 'sppearce/sention_tnhaplotyper2_nftest' into sention_tnhaplotyper2_nftest
SPPearce
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Merge branch 'master' into sention_tnhaplotyper2_nftest
SPPearce
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Update snapshots
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committed
Update snapshots
SPPearce
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Merge remote-tracking branch 'sppearce/sention_tnhaplotyper2_nftest' into sention_tnhaplotyper2_nftest
SPPearce
committed

Commits on Apr 17, 2025

Update modules/nf-core/sentieon/tnhaplotyper2/main.nf

SPPearce
and
LouisLeNezet
authored

Commits on Apr 18, 2025