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Plant-Food-Research-Open / genepal Public

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Added liftoff, integrated with pfr/nxf-modules, and some minor improvements#2

Merged

GallVp merged 59 commits intomainPlant-Food-Research-Open/genepal:mainfrom devPlant-Food-Research-Open/genepal:devCopy head branch name to clipboard

Jan 11, 2024

+7,857-1,812

Conversation Commits59 (59)Checks Files changed

Commits

Commits on Jan 11, 2024

Added updated info about nf-core modules
GallVp
committed
Turned off SortMeRNA by default
GallVp
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Decouple target assemblies and read qc/align
GallVp
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A bit of reformatiing
GallVp
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Started implementing liftoff
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Checkpoint before major reshuffle
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Reformatted local modules
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Now using galaxy containers
GallVp
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Extracted some subworkflows
GallVp
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Extracted a few subworkflows
GallVp
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Extracted subworkflows uptill BRAKER3
GallVp
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Inc liftoff
GallVp
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Added polished out channel to liftoff
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Added gffread before liftoff
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Updated flowchart
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Added liftoff options
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Started moving to nf-core/tools
GallVp
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Reimported modules using nf-core/tools
GallVp
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Reimported kherronism modules with nf-core/tools
GallVp
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Updated braker3
GallVp
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Updated repeatmasker
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Updated modules
GallVp
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Imported fastavalidate and liftoff from pfr/nxf-modules
GallVp
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Updated modules and subworkflows
GallVp
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Added EDTA from pfr/nxf-modules
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Updated config
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Integrated fastavalidator
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Added patch for star/genomegenerate
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Incorporated fasta_edta_lai
GallVp
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Trying to add FASTQ_FASTQC_UMITOOLS_FASTP
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Updated modules and applied prettier
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FASTP now has stub
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SORTMERNA now has stub
GallVp
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Cleaned up prepare_assembly
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Cleaned up preprocess_rnaseq
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Reformatted and inc ALIGN_RNASEQ
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Cleaned up and inc PREPARE_EXT_PROTS
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Cleanedup BRAKER3
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Updated fastp, sortmerna and liftoff
GallVp
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Cleaned up fasta_liftoff
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Updated fasta_edta_lai
GallVp
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Added script for local stub run
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Samplesheet now accepts relative paths
GallVp
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Updated modules
GallVp
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Removed -exclude_partial and updated flowchart
GallVp
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Separated test config for local and pfr
GallVp
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Fixed local script typo
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Fixed apptainer scope bug in base config
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Updated README
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Readded -exclude_partial and now using teambraker container
GallVp
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Added config for test data and quay.io container for braker3
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Now using repeatmodeler by default
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BRAKER3 now runnable with test data
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Added editor config
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Disabled sortmerna by default added option to save cat bam
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Added pre-commit
GallVp
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Updated manifest
GallVp
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Fixed linting errors
GallVp
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Updated base config for docker
GallVp
committed

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