`SHAPEIT5_PHASERARE` Migrate to nf-test#7064

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LouisLeNezet wants to merge 58 commits intonf-core:masterfrom LouisLeNezet:shapeit5_phaserare

+12,042-3,272

Commits on Nov 22, 2024

Migrate to nf-test
LouisLeNezet
committed
Update tags
LouisLeNezet
committed
Merge branch 'master' into shapeit5_phaserare
LouisLeNezet
authored

Commits on Nov 23, 2024

Merge branch 'master' into shapeit5_phaserare
LouisLeNezet
authored

Commits on Nov 25, 2024

Merge branch 'master' into shapeit5_phaserare
LouisLeNezet
authored

Commits on Dec 4, 2024

trgt/merge: Made extension of stub test configurable (nf-core#7080 )

Schmytzi
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LouisLeNezet
committed
Fix output channel of TCOFFEE/CONSENSUS (nf-core#7082 )

luisas
authored and
LouisLeNezet
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homer groseq update (nf-core#7073 )

edmundmiller
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LouisLeNezet
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ci: Just lint all the subworkflows (nf-core#7084 )

edmundmiller
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LouisLeNezet
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New module: COPTR/MERGE (nf-core#7062 )

authored and
LouisLeNezet
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remove soft-linking of fasta instead stage in dir (nf-core#7081 )

sateeshperi
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LouisLeNezet
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bismark/align - use more descriptive variable names than it in test (nf-core#7035 )

authored and
LouisLeNezet
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Fix tcoffee alncompare (nf-core#7048 )

luisas
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LouisLeNezet
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Fix input tree in CLUSTALO/ALIGN (nf-core#7092 )

luisas
authored and
LouisLeNezet
committed
BCFTOOLS_CONVERT Migration to nf-test (nf-core#7049 )

committed
Pydamage change output file name (nf-core#7095 )

authored and
LouisLeNezet
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Added four file params to clustalo/align (nf-core#7093 )

authored and
LouisLeNezet
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Bump GUNC and add gunc/run test (nf-core#6920 )

authored and
LouisLeNezet
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Added subworkflow fasta_gxf_busco_plot (nf-core#7051 )

authored and
LouisLeNezet
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Fasta index bismark bwameth (nf-core#7010 )

authored and
LouisLeNezet
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update malt/build module (nf-core#6994 )

authored and
LouisLeNezet
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Add mafft guidetree (nf-core#7097 )

authored and
LouisLeNezet
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fix versions of mafft/guidetree (nf-core#7104 )

luisas
authored and
LouisLeNezet
committed
Fix prettier mafft (nf-core#7110 )

luisas
authored and
LouisLeNezet
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Update trinity version (nf-core#7109 )

authored and
LouisLeNezet
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Add module gzrt (nf-core#6918 ) (nf-core#7052 )

authored and
LouisLeNezet
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adding mgikit module (nf-core#7008 )

authored and
LouisLeNezet
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Add sylph sketch (nf-core#7078 )

authored and
LouisLeNezet
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Update hifiasm (nf-core#7114 )

fellen31
authored and
LouisLeNezet
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Attempt at fixing samshee module with latest release (nf-core#7117 )

apeltzer
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LouisLeNezet
committed
Add compressed output support for GAWK (nf-core#7105 )

LouisLeNezet
and
LouisLeNezet
committed
spaceranger_bump_version (nf-core#7088 )

authored and
LouisLeNezet
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update module propr/propd (nf-core#7083 )

suzannejin
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LouisLeNezet
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New Module: NACHO_NORMALISE (nf-core#7100 )

authored and
LouisLeNezet
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New Module: NACHO_QC (nf-core#7108 )

alanmmobbs93
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LouisLeNezet
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UMICollapse module: Drop external dependencies from UMICollapse module tests (nf-core#7075 )

authored and
LouisLeNezet
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Add module muse/call (nf-core#5630 )

famosab
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LouisLeNezet
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Remove unused code from utils_nfcore_pipeline swf (nf-core#7094 )

mirpedrol
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LouisLeNezet
committed
fix linting on meta.yml files (nf-core#7121 )

alanmmobbs93
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LouisLeNezet
committed
Add name to SYLPH_SKETCH module tests (nf-core#7122 )

pinin4fjords
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LouisLeNezet
committed
Fastq align dedup bwameth (nf-core#7007 )

authored and
LouisLeNezet
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use just MemoryUnit as per language server reco (nf-core#7127 )

sateeshperi
authored and
LouisLeNezet
committed
checkm/qa: Improve input validation (nf-core#7119 )

authored and
LouisLeNezet
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new module plink genome (nf-core#7112 )

authored and
LouisLeNezet
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Lint fastqs before and during preprocessing (nf-core#7123 )

authored and
LouisLeNezet
committed
Fix bug in RRNATRANSCRIPTS with harcoded gtf (nf-core#7141 )

atrigila
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LouisLeNezet
committed
Switch featureCounts to TSV (nf-core#7136 )

edmundmiller
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LouisLeNezet
committed
Add module muse/sump (nf-core#5629 )

authored and
LouisLeNezet
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Add clustalo as aligner to fasta_newick_epang_gappa swf (nf-core#7099 )

authored and
LouisLeNezet
committed
New module: COPTR/EXTRACT (nf-core#7089 )

authored and
LouisLeNezet
committed
Minor fixes to linting in prepro (nf-core#7144 )

pinin4fjords
authored and
LouisLeNezet
committed
Minor refactor on attachMultiqcReport function. (nf-core#7129 )

authored and
LouisLeNezet
committed
SHAPEIT5_PHASECOMMON Migrate to nf-test (nf-core#7061 )

committed
Convert exception obj to string (nf-core#7148 )

nschcolnicov
authored and
LouisLeNezet
committed
Increase default resource allocation for Ribotracer prepareorfs (nf-core#7145 )

FelixKrueger
authored and
LouisLeNezet
committed
New module: COPTR/ESTIMATE (nf-core#7149 )

authored and
LouisLeNezet
committed
Cellbender empty droplet removal (nf-core#7031 )

chaochaowong
authored and
LouisLeNezet
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Change GLIMPSE2_concordance non mandatory values (nf-core#7146 )

authored and
LouisLeNezet
committed