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# .github/CODEOWNERS auto-generated by scripts/generate_codeowners.py
#
# Owners were reconstructed from git history + .dockstore.yml authors and
# mapped to GitHub handles best-effort.
# Anybody is free to add their name here
# --- amplicon ---
/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/ @RZ9082 @MaraBesemer @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-its/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-single-end/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-rrna-prediction/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/mgnify-amplicon-taxonomic-summary-tables/ @RZ9082 @paulzierep
/workflows/amplicon/amplicon-mgnify/taxonomic-rank-abundance-summary-table/ @RZ9082 @paulzierep
/workflows/amplicon/dada2/ @bernt-matthias
/workflows/amplicon/qiime2/qiime2-I-import/ @debjyoti197 @bernt-matthias
/workflows/amplicon/qiime2/qiime2-II-denoising/ @debjyoti197 @bernt-matthias
/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/ @debjyoti197 @bernt-matthias
# --- bacterial_genomics ---
/workflows/bacterial_genomics/amr_gene_detection/ @clsiguret @hugolefeuvre # also: Pierre Marin <0000-0002-8304-138X>
/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/ @clsiguret @hugolefeuvre # also: Pierre Marin <0000-0002-8304-138X>
/workflows/bacterial_genomics/bacterial_genome_annotation/ @clsiguret @hugolefeuvre # also: Pierre Marin <0000-0002-8304-138X>
/workflows/bacterial_genomics/cgmlst-bacterial-genome/ @clsiguret @hugolefeuvre
# --- comparative_genomics ---
/workflows/comparative_genomics/hyphy/ @d-callan @SPond # also: Hannah Verdonk <0000-0003-1967-4403>
# --- computational-chemistry ---
/workflows/computational-chemistry/fragment-based-docking-scoring/ @simonbray # also: Tim Dudgeon <0000-0001-6879-5194>
/workflows/computational-chemistry/gromacs-dctmd/ @simonbray
/workflows/computational-chemistry/gromacs-mmgbsa/ @simonbray
/workflows/computational-chemistry/protein-ligand-complex-parameterization/ @simonbray
# --- data-fetching ---
/workflows/data-fetching/parallel-accession-download/ @mvdbeek @lldelisle
/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/ @lldelisle @wm75 # also: Pierre Osteil <0000-0002-5832-6703>
# --- epigenetics ---
/workflows/epigenetics/atacseq/ @lldelisle
/workflows/epigenetics/average-bigwig-between-replicates/ @lldelisle
/workflows/epigenetics/chipseq-pe/ @lldelisle
/workflows/epigenetics/chipseq-sr/ @lldelisle @pavanvidem
/workflows/epigenetics/consensus-peaks/ @lldelisle
/workflows/epigenetics/cutandrun/ @lldelisle
/workflows/epigenetics/hic-hicup-cooler/ @lldelisle
# --- genome-assembly ---
/workflows/genome-assembly/assembly-with-flye/ @AnnaSyme
/workflows/genome-assembly/bacterial-genome-assembly/ @clsiguret @hugolefeuvre # also: Pierre Marin <0000-0002-8304-138X>
/workflows/genome-assembly/polish-with-long-reads/ @AnnaSyme
/workflows/genome-assembly/quality-and-contamination-control-raw-reads/ @clsiguret @hugolefeuvre # also: Pierre Marin <0000-0002-8304-138X>
# --- genome_annotation ---
/workflows/genome_annotation/annotation-braker3/ @rlibouba
/workflows/genome_annotation/annotation-helixer/ @rlibouba
/workflows/genome_annotation/annotation-maker/ @rlibouba
/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/ @rlibouba @abretaud @SantaMcCloud
/workflows/genome_annotation/lncRNAs-annotation/ @rlibouba
# --- imaging ---
/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/ @kostrykin
/workflows/imaging/histological-staining-area-quantification/ @dianichj
/workflows/imaging/tissue-microarray-analysis/multiplex-tissue-microarray-analysis/ @CameronFRWatson
/workflows/imaging/tissue-microarray-analysis/tissue-microarray-analysis/ @CameronFRWatson
# --- metabolomics ---
/workflows/metabolomics/gcms-metams/ @hechth
/workflows/metabolomics/lcms-preprocessing/ @hechth
/workflows/metabolomics/mfassignr/ @hechth # also: Kristina Gomoryova <0000-0003-4407-3917>
/workflows/metabolomics/qcxms-sdf/ @hechth
# --- microbiome ---
/workflows/microbiome/binning-evaluation/ @SantaMcCloud
/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/ @paulzierep @bebatut
/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/ @paulzierep @bebatut @Minamehr
/workflows/microbiome/mag-genome-annotation-parallel/ @paulzierep @SantaMcCloud
/workflows/microbiome/mags-building/ @paulzierep @bebatut @Minamehr @SantaMcCloud # also: Patrick Bühler <0000-0003-2982-388X>
/workflows/microbiome/mags-taxonomy-annotation/ @SantaMcCloud @gdefazio
/workflows/microbiome/metagenomic-genes-catalogue/ @hugolefeuvre
/workflows/microbiome/metagenomic-raw-reads-amr-analysis/ @hugolefeuvre
/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/ @engynasr @bebatut @paulzierep
/workflows/microbiome/pathogen-identification/gene-based-pathogen-identification/ @engynasr @bebatut @paulzierep
/workflows/microbiome/pathogen-identification/nanopore-pre-processing/ @bebatut @engynasr @paulzierep
/workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/ @engynasr @bebatut @paulzierep
/workflows/microbiome/pathogen-identification/taxonomy-profiling-and-visualization-with-krona/ @engynasr @bebatut @paulzierep
# --- proteomics ---
/workflows/proteomics/clinicalmp/clinicalmp-data-interpretation/ @katherine-d21
/workflows/proteomics/clinicalmp/clinicalmp-database-generation/ @subinamehta
/workflows/proteomics/clinicalmp/clinicalmp-discovery/ @subinamehta
/workflows/proteomics/clinicalmp/clinicalmp-quantitation/ @subinamehta
/workflows/proteomics/clinicalmp/clinicalmp-verification/ @PratikDJagtap
/workflows/proteomics/openms-metaprosip/ @bernt-matthias
# --- read-preprocessing ---
/workflows/read-preprocessing/short-read-qc-trimming/ @bebatut @paulzierep
# --- repeatmasking ---
/workflows/repeatmasking/ @rlibouba
# --- sars-cov-2-variant-calling ---
/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/ @wm75
/workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ @wm75
/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/ @pvanheus @wm75
/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/ @wm75 @drosofff
/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/ @wm75 @drosofff
/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/ @wm75
/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/ @wm75
# --- scRNAseq ---
/workflows/scRNAseq/baredsc/ @lldelisle
/workflows/scRNAseq/fastq-to-matrix-10x/ @lldelisle @mtekman @hrhotz @blankenberg @nomadscientist @pavanvidem
/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/ @dianichj @pavanvidem @pcm32
/workflows/scRNAseq/scanpy-clustering/ @pavanvidem @hrhotz @mtekman @bebatut
/workflows/scRNAseq/velocyto/ @lldelisle
# --- transcriptomics ---
/workflows/transcriptomics/brew3r/ @lldelisle
/workflows/transcriptomics/goseq/ @nilchia
/workflows/transcriptomics/rnaseq-de/ @pavanvidem
/workflows/transcriptomics/rnaseq-pe/ @lldelisle @pavanvidem
/workflows/transcriptomics/rnaseq-sr/ @lldelisle @pavanvidem
# --- variant-calling ---
/workflows/variant-calling/generic-variant-calling-wgs-pe/ @nekrut
/workflows/variant-calling/haploid-variant-calling-wgs-pe/ @nekrut
/workflows/variant-calling/ploidy-aware-genotype-calling/ @SaimMomin12 @wm75
/workflows/variant-calling/variation-reporting/ @wm75
# --- virology ---
/workflows/virology/generic-non-segmented-viral-variant-calling/ @pvanheus @wm75
/workflows/virology/influenza-isolates-consensus-and-subtyping/ @kciy @wm75 @SaimMomin12 # also: Aaron Kolbecher <0009-0000-8844-2812>
/workflows/virology/pox-virus-amplicon/ @kciy @wm75
## --- VGP-assembly-v2 ---
/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/ @Delphine-L
/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/ @Delphine-L
/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/ @Delphine-L
/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/ @Delphine-L
/workflows/VGP-assembly-v2/Plot-Nx-Size/ @Delphine-L
/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/ @Delphine-L
/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/ @Delphine-L
/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/ @Delphine-L
/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/ @smeds @Delphine-L
/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/ @Delphine-L
/workflows/VGP-assembly-v2/post-curation-processing/ @Delphine-L
# --- VGP-assembly-v2 ---
/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/ @Delphine-L
/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/ @Delphine-L
/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/ @Delphine-L
/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/ @Delphine-L
/workflows/VGP-assembly-v2/Plot-Nx-Size/ @Delphine-L
/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/ @Delphine-L
/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/ @Delphine-L
/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/ @Delphine-L
/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/ @smeds @Delphine-L
/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/ @Delphine-L @nekrut
/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/ @Delphine-L
/workflows/VGP-assembly-v2/post-curation-processing/ @Delphine-L