diff --git a/src/annotate/celltypist/config.vsh.yaml b/src/annotate/celltypist/config.vsh.yaml index 0812766949a..e71ebe9b4f2 100644 --- a/src/annotate/celltypist/config.vsh.yaml +++ b/src/annotate/celltypist/config.vsh.yaml @@ -5,8 +5,6 @@ description: Automated cell type annotation tool for scRNA-seq datasets on the b authors: - __merge__: /src/authors/jakub_majercik.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] argument_groups: - name: Inputs diff --git a/src/annotate/scanvi/config.vsh.yaml b/src/annotate/scanvi/config.vsh.yaml index 4c1f91253ca..dffcfa4963b 100644 --- a/src/annotate/scanvi/config.vsh.yaml +++ b/src/annotate/scanvi/config.vsh.yaml @@ -7,11 +7,9 @@ description: | authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/jakub_majercik.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] argument_groups: - name: Inputs arguments: diff --git a/src/annotate/singler/config.vsh.yaml b/src/annotate/singler/config.vsh.yaml index 81646680c6f..df05995aa83 100644 --- a/src/annotate/singler/config.vsh.yaml +++ b/src/annotate/singler/config.vsh.yaml @@ -9,8 +9,6 @@ description: | authors: - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] argument_groups: - name: Inputs diff --git a/src/authors/angela_pisco.yaml b/src/authors/angela_pisco.yaml index 2b7e9104f44..4b43ef04dfd 100644 --- a/src/authors/angela_pisco.yaml +++ b/src/authors/angela_pisco.yaml @@ -1,14 +1,6 @@ name: Angela Oliveira Pisco info: - role: Contributor links: github: aopisco orcid: "0000-0003-0142-2355" linkedin: aopisco - organizations: - - name: Insitro - href: https://insitro.com - role: Director of Computational Biology - - name: Open Problems - href: https://openproblems.bio - role: Core Member \ No newline at end of file diff --git a/src/authors/dorien_roosen.yaml b/src/authors/dorien_roosen.yaml index 96bb9d37fbb..4c96d3a23d1 100644 --- a/src/authors/dorien_roosen.yaml +++ b/src/authors/dorien_roosen.yaml @@ -1,11 +1,6 @@ name: Dorien Roosen info: - role: Core Team Member links: - email: dorien@data-intuitive.com github: dorien-er + orcid: 0000-0002-6261-8151 linkedin: dorien-roosen - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Data Scientist \ No newline at end of file diff --git a/src/authors/dries_de_maeyer.yaml b/src/authors/dries_de_maeyer.yaml index dc67ecca964..99536ed8162 100644 --- a/src/authors/dries_de_maeyer.yaml +++ b/src/authors/dries_de_maeyer.yaml @@ -1,11 +1,5 @@ name: Dries De Maeyer info: - role: Core Team Member links: - email: ddemaeyer@gmail.com github: ddemaeyer linkedin: dries-de-maeyer-b46a814 - organizations: - - name: Janssen Pharmaceuticals - href: https://www.janssen.com - role: Principal Scientist \ No newline at end of file diff --git a/src/authors/dries_schaumont.yaml b/src/authors/dries_schaumont.yaml index fc28b844650..5873fc867c6 100644 --- a/src/authors/dries_schaumont.yaml +++ b/src/authors/dries_schaumont.yaml @@ -1,12 +1,5 @@ name: Dries Schaumont info: - role: Core Team Member links: - email: dries@data-intuitive.com github: DriesSchaumont orcid: "0000-0002-4389-0440" - linkedin: dries-schaumont - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Data Scientist \ No newline at end of file diff --git a/src/authors/elizabeth_mlynarski.yaml b/src/authors/elizabeth_mlynarski.yaml deleted file mode 100644 index 9e59872d42c..00000000000 --- a/src/authors/elizabeth_mlynarski.yaml +++ /dev/null @@ -1,6 +0,0 @@ -name: Elizabeth Mlynarski -info: - role: Contributor - organizations: - - name: Janssen R&D US - role: Principal Scientist Computational Genomics \ No newline at end of file diff --git a/src/authors/isabelle_bergiers.yaml b/src/authors/isabelle_bergiers.yaml index 64e958593db..21bfbdca0f5 100644 --- a/src/authors/isabelle_bergiers.yaml +++ b/src/authors/isabelle_bergiers.yaml @@ -1,10 +1,5 @@ name: Isabelle Bergiers info: - role: Contributor links: github: Isabelle-b orcid: 0000-0001-9622-7960 - organizations: - - name: Janssen Pharmaceuticals - href: https://www.janssen.com - role: Scientist OMICS Technology \ No newline at end of file diff --git a/src/authors/jakub_majercik.yaml b/src/authors/jakub_majercik.yaml index b1086deee2d..bb4bcc1f97c 100644 --- a/src/authors/jakub_majercik.yaml +++ b/src/authors/jakub_majercik.yaml @@ -1,11 +1,5 @@ name: Jakub Majercik info: - role: Contributor links: - email: jakub@data-intuitive.com github: jakubmajercik linkedin: jakubmajercik - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Bioinformatics Engineer \ No newline at end of file diff --git a/src/authors/kai_waldrant.yaml b/src/authors/kai_waldrant.yaml index 2ba24891b6d..d07ff82426a 100644 --- a/src/authors/kai_waldrant.yaml +++ b/src/authors/kai_waldrant.yaml @@ -1,15 +1,6 @@ name: Kai Waldrant info: - role: Contributor links: - email: kai@data-intuitive.com github: KaiWaldrant orcid: "0009-0003-8555-1361" linkedin: kaiwaldrant - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Bioinformatician - - name: Open Problems - href: https://openproblems.bio - role: Contributor diff --git a/src/authors/luke_zappia.yaml b/src/authors/luke_zappia.yaml index ad767e33f86..2083c63be5c 100644 --- a/src/authors/luke_zappia.yaml +++ b/src/authors/luke_zappia.yaml @@ -1,12 +1,6 @@ name: Luke Zappia info: - role: Contributor links: - email: luke@data-intuitive.com github: lazappi orcid: 0000-0001-7744-8565 linkedin: lazappi - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Data Science Engineer diff --git a/src/authors/malte_luecken.yaml b/src/authors/malte_luecken.yaml index ab6357cfd70..e25efcd76b3 100644 --- a/src/authors/malte_luecken.yaml +++ b/src/authors/malte_luecken.yaml @@ -1,16 +1,6 @@ name: Malte D. Luecken info: - role: Core Team Member links: - email: malte.luecken@helmholtz-muenchen.de github: LuckyMD orcid: "0000-0001-7464-7921" linkedin: malte-l%C3%BCcken-b8b21049 - twitter: MDLuecken - organizations: - - name: Helmholtz Munich - href: https://www.helmholtz-munich.de - role: Group Leader - - name: Open Problems - href: https://openproblems.bio - role: Core Member \ No newline at end of file diff --git a/src/authors/marijke_van_moerbeke.yaml b/src/authors/marijke_van_moerbeke.yaml index bfdd96eab1c..9f6f91b6087 100644 --- a/src/authors/marijke_van_moerbeke.yaml +++ b/src/authors/marijke_van_moerbeke.yaml @@ -1,11 +1,6 @@ name: Marijke Van Moerbeke info: - role: Contributor links: github: mvanmoerbeke orcid: 0000-0002-3097-5621 linkedin: marijke-van-moerbeke-84303a34 - organizations: - - name: OpenAnalytics - href: https://www.openanalytics.eu - role: Statistical Consultant \ No newline at end of file diff --git a/src/authors/matthias_beyens.yaml b/src/authors/matthias_beyens.yaml index b2f80ce8789..a49a2a65ba1 100644 --- a/src/authors/matthias_beyens.yaml +++ b/src/authors/matthias_beyens.yaml @@ -1,12 +1,6 @@ name: Matthias Beyens info: - role: Contributor links: github: MatthiasBeyens orcid: "0000-0003-3304-0706" - email: matthias.beyens@gmail.com linkedin: mbeyens - organizations: - - name: Janssen Pharmaceuticals - href: https://www.janssen.com - role: Principal Scientist \ No newline at end of file diff --git a/src/authors/mauro_saporita.yaml b/src/authors/mauro_saporita.yaml index 3cd7b06a870..146212fdc5a 100644 --- a/src/authors/mauro_saporita.yaml +++ b/src/authors/mauro_saporita.yaml @@ -1,11 +1,5 @@ name: Mauro Saporita info: - role: Contributor links: - email: maurosaporita@gmail.com github: mauro-saporita linkedin: mauro-saporita-930b06a5 - organizations: - - name: Ardigen - href: https://ardigen.com - role: Lead Nextflow Developer \ No newline at end of file diff --git a/src/authors/povilas_gibas.yaml b/src/authors/povilas_gibas.yaml index d438f9eccf4..6f6c74c5f27 100644 --- a/src/authors/povilas_gibas.yaml +++ b/src/authors/povilas_gibas.yaml @@ -1,11 +1,5 @@ name: Povilas Gibas info: - role: Contributor links: - email: povilasgibas@gmail.com github: PoGibas linkedin: povilas-gibas - organizations: - - name: Ardigen - href: https://ardigen.com - role: Bioinformatician \ No newline at end of file diff --git a/src/authors/robrecht_cannoodt.yaml b/src/authors/robrecht_cannoodt.yaml index eb6305b8321..220cc853959 100644 --- a/src/authors/robrecht_cannoodt.yaml +++ b/src/authors/robrecht_cannoodt.yaml @@ -1,15 +1,6 @@ name: Robrecht Cannoodt info: - role: Core Team Member links: - email: robrecht@data-intuitive.com github: rcannood orcid: "0000-0003-3641-729X" linkedin: robrechtcannoodt - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Data Science Engineer - - name: Open Problems - href: https://openproblems.bio - role: Core Member \ No newline at end of file diff --git a/src/authors/samuel_d_souza.yaml b/src/authors/samuel_d_souza.yaml index 2c7ff474b7b..7a268a571e7 100644 --- a/src/authors/samuel_d_souza.yaml +++ b/src/authors/samuel_d_souza.yaml @@ -1,10 +1,5 @@ name: Samuel D'Souza info: - role: Contributor links: github: srdsam linkedin: samuel-d-souza-887023150/ - organizations: - - name: Chan Zuckerberg Biohub - href: https://www.czbiohub.org - role: Data Engineer \ No newline at end of file diff --git a/src/authors/sarah_ouologuem.yaml b/src/authors/sarah_ouologuem.yaml index 5ed8795a5d2..bb14e0ca7e6 100644 --- a/src/authors/sarah_ouologuem.yaml +++ b/src/authors/sarah_ouologuem.yaml @@ -1,10 +1,5 @@ name: Sarah Ouologuem info: - role: Contributor links: github: SarahOuologuem orcid: 0009-0005-3398-1700 - organizations: - - name: Helmholtz Munich - href: https://www.helmholtz-munich.de - role: Student Assistant \ No newline at end of file diff --git a/src/authors/toni_verbeiren.yaml b/src/authors/toni_verbeiren.yaml index aa78550db54..1154acf88b4 100644 --- a/src/authors/toni_verbeiren.yaml +++ b/src/authors/toni_verbeiren.yaml @@ -1,10 +1,5 @@ name: Toni Verbeiren info: - role: Core Team Member links: github: tverbeiren linkedin: verbeiren - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Data Scientist and CEO \ No newline at end of file diff --git a/src/authors/vladimir_shitov.yaml b/src/authors/vladimir_shitov.yaml index 9dfe8227f7c..85ca9a74bbb 100644 --- a/src/authors/vladimir_shitov.yaml +++ b/src/authors/vladimir_shitov.yaml @@ -1,12 +1,6 @@ name: Vladimir Shitov info: - role: Contributor links: - email: vladimir.shitov@helmholtz-muenchen.de github: vladimirshitov orcid: "0000-0002-1960-8812" linkedin: vladimir-shitov-9a659513b - organizations: - - name: Helmholtz Munich - href: https://www.helmholtz-munich.de - role: PhD Candidate \ No newline at end of file diff --git a/src/authors/weiwei_schultz.yaml b/src/authors/weiwei_schultz.yaml deleted file mode 100644 index 7d4835e89d5..00000000000 --- a/src/authors/weiwei_schultz.yaml +++ /dev/null @@ -1,6 +0,0 @@ -name: Weiwei Schultz -info: - role: Contributor - organizations: - - name: Janssen R&D US - role: Associate Director Data Sciences \ No newline at end of file diff --git a/src/authors/xichen_wu.yaml b/src/authors/xichen_wu.yaml index 935851abcca..7adcbb82c25 100644 --- a/src/authors/xichen_wu.yaml +++ b/src/authors/xichen_wu.yaml @@ -1,11 +1,6 @@ name: Xichen Wu info: - role: Contributor links: github: wxicu linkedin: xichen-wu orcid: 0009-0008-2168-4508 - organizations: - - name: Helmholtz Munich - href: https://www.helmholtz-munich.de - role: Student Assistant \ No newline at end of file diff --git a/src/cluster/leiden/config.vsh.yaml b/src/cluster/leiden/config.vsh.yaml index 0133210d73e..00c5bd0b590 100644 --- a/src/cluster/leiden/config.vsh.yaml +++ b/src/cluster/leiden/config.vsh.yaml @@ -13,7 +13,7 @@ description: | [Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] arguments: # input - name: "--input" diff --git a/src/compression/compress_h5mu/config.vsh.yaml b/src/compression/compress_h5mu/config.vsh.yaml index 64ca34a55dc..2fde27cf20a 100644 --- a/src/compression/compress_h5mu/config.vsh.yaml +++ b/src/compression/compress_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Compress a MuData file. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_10xh5_to_h5mu/config.vsh.yaml b/src/convert/from_10xh5_to_h5mu/config.vsh.yaml index f494fca1f13..85bf77e78ca 100644 --- a/src/convert/from_10xh5_to_h5mu/config.vsh.yaml +++ b/src/convert/from_10xh5_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts a 10x h5 into an h5mu file. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml b/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml index 13f9024ad23..3e0d53c3e03 100644 --- a/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml +++ b/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts a 10x mtx into an h5mu file. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml b/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml index d4b94820d1c..56853451a8d 100644 --- a/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml +++ b/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB). authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml b/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml index 3968e7b7f9c..2fe6c120b45 100644 --- a/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml +++ b/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ author ] argument_groups: diff --git a/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml b/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml index 2bc45597e80..b649cc8cd90 100644 --- a/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml +++ b/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml @@ -19,7 +19,7 @@ description: | Currently does not allow parsing the output from cell barcode demultiplexing. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_h5ad_to_h5mu/config.vsh.yaml b/src/convert/from_h5ad_to_h5mu/config.vsh.yaml index 33c43d7cb54..58b6732d93b 100644 --- a/src/convert/from_h5ad_to_h5mu/config.vsh.yaml +++ b/src/convert/from_h5ad_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts a single layer h5ad file into a single MuData object authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_h5ad_to_seurat/config.vsh.yaml b/src/convert/from_h5ad_to_seurat/config.vsh.yaml index 8ae6f339e79..bc04770951e 100644 --- a/src/convert/from_h5ad_to_seurat/config.vsh.yaml +++ b/src/convert/from_h5ad_to_seurat/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts an h5ad file into a Seurat file. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_h5mu_or_h5ad_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_or_h5ad_to_seurat/config.vsh.yaml index 2823d29be97..1bf96da0ad7 100644 --- a/src/convert/from_h5mu_or_h5ad_to_seurat/config.vsh.yaml +++ b/src/convert/from_h5mu_or_h5ad_to_seurat/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts an h5ad file or a single modality of an h5mu file into a Seurat file. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_h5mu_or_h5ad_to_tiledb/config.vsh.yaml b/src/convert/from_h5mu_or_h5ad_to_tiledb/config.vsh.yaml index b49808f1619..9ebbdaec538 100644 --- a/src/convert/from_h5mu_or_h5ad_to_tiledb/config.vsh.yaml +++ b/src/convert/from_h5mu_or_h5ad_to_tiledb/config.vsh.yaml @@ -7,7 +7,7 @@ description: | NOTE: The functionality provided by this component is experimental and may be subject to change. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: "Input" arguments: diff --git a/src/convert/from_h5mu_to_h5ad/config.vsh.yaml b/src/convert/from_h5mu_to_h5ad/config.vsh.yaml index 7570d306a00..5c6f1b88c21 100644 --- a/src/convert/from_h5mu_to_h5ad/config.vsh.yaml +++ b/src/convert/from_h5mu_to_h5ad/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts a h5mu file into a h5ad file. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_h5mu_to_seurat/config.vsh.yaml b/src/convert/from_h5mu_to_seurat/config.vsh.yaml index bad9a3681ca..503102fbdca 100644 --- a/src/convert/from_h5mu_to_seurat/config.vsh.yaml +++ b/src/convert/from_h5mu_to_seurat/config.vsh.yaml @@ -13,7 +13,7 @@ description: | - Seurat does not support global variables metadata /var. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/convert/from_seurat_to_h5mu/config.vsh.yaml b/src/convert/from_seurat_to_h5mu/config.vsh.yaml index 46d4560b317..4b45f48f350 100644 --- a/src/convert/from_seurat_to_h5mu/config.vsh.yaml +++ b/src/convert/from_seurat_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Converts a Seurat file into an H5MU file. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/convert/from_tiledb_to_h5mu/config.vsh.yaml b/src/convert/from_tiledb_to_h5mu/config.vsh.yaml index fcb548abce4..ddb7f5e29f4 100644 --- a/src/convert/from_tiledb_to_h5mu/config.vsh.yaml +++ b/src/convert/from_tiledb_to_h5mu/config.vsh.yaml @@ -3,7 +3,7 @@ namespace: convert scope: public authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input database description: "Open a tileDB-SOMA database by URI." diff --git a/src/dataflow/concatenate_h5mu/config.vsh.yaml b/src/dataflow/concatenate_h5mu/config.vsh.yaml index 84589ac3bba..51aea77a9ce 100644 --- a/src/dataflow/concatenate_h5mu/config.vsh.yaml +++ b/src/dataflow/concatenate_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/dataflow/merge/config.vsh.yml b/src/dataflow/merge/config.vsh.yml index 4200d2d54b9..6a4fba55fd8 100644 --- a/src/dataflow/merge/config.vsh.yml +++ b/src/dataflow/merge/config.vsh.yml @@ -5,7 +5,7 @@ description: | Combine one or more single-modality .h5mu files together into one .h5mu file. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/dataflow/split_h5mu/config.vsh.yaml b/src/dataflow/split_h5mu/config.vsh.yaml index fbfe373067d..0039b12733f 100644 --- a/src/dataflow/split_h5mu/config.vsh.yaml +++ b/src/dataflow/split_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input & specifications arguments: diff --git a/src/dataflow/split_modalities/config.vsh.yaml b/src/dataflow/split_modalities/config.vsh.yaml index 3ada61f2717..fc671c9828d 100644 --- a/src/dataflow/split_modalities/config.vsh.yaml +++ b/src/dataflow/split_modalities/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor ] arguments: diff --git a/src/demux/bcl2fastq/config.vsh.yaml b/src/demux/bcl2fastq/config.vsh.yaml index d260d9fdcee..d198dc3a440 100644 --- a/src/demux/bcl2fastq/config.vsh.yaml +++ b/src/demux/bcl2fastq/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Convert bcl files to fastq files using bcl2fastq. authors: - __merge__: /src/authors/toni_verbeiren.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: [ "-i", "--runfolder_dir" ] diff --git a/src/demux/bcl_convert/config.vsh.yaml b/src/demux/bcl_convert/config.vsh.yaml index 6c571a6b523..e8fffe950de 100644 --- a/src/demux/bcl_convert/config.vsh.yaml +++ b/src/demux/bcl_convert/config.vsh.yaml @@ -8,11 +8,9 @@ description: | and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html authors: - __merge__: /src/authors/toni_verbeiren.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/marijke_van_moerbeke.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] arguments: diff --git a/src/demux/cellranger_mkfastq/config.vsh.yaml b/src/demux/cellranger_mkfastq/config.vsh.yaml index fd1eb572f23..3101c2e4271 100644 --- a/src/demux/cellranger_mkfastq/config.vsh.yaml +++ b/src/demux/cellranger_mkfastq/config.vsh.yaml @@ -13,7 +13,7 @@ authors: - __merge__: /src/authors/samuel_d_souza.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - type: file name: --input diff --git a/src/differential_expression/create_pseudobulk/config.vsh.yaml b/src/differential_expression/create_pseudobulk/config.vsh.yaml index cef07f3afef..3b14d61bc3e 100644 --- a/src/differential_expression/create_pseudobulk/config.vsh.yaml +++ b/src/differential_expression/create_pseudobulk/config.vsh.yaml @@ -14,10 +14,6 @@ authors: roles: [ author ] - __merge__: /src/authors/jakub_majercik.yaml roles: [ author ] - - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ contributor ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] argument_groups: - name: Inputs diff --git a/src/differential_expression/deseq2/config.vsh.yaml b/src/differential_expression/deseq2/config.vsh.yaml index dcc6856d7d0..80b36f92408 100644 --- a/src/differential_expression/deseq2/config.vsh.yaml +++ b/src/differential_expression/deseq2/config.vsh.yaml @@ -9,10 +9,6 @@ authors: roles: [ author ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] - - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ contributor ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] argument_groups: - name: Inputs diff --git a/src/dimred/densmap/config.vsh.yaml b/src/dimred/densmap/config.vsh.yaml index 1282052c29c..24de25ffb00 100644 --- a/src/dimred/densmap/config.vsh.yaml +++ b/src/dimred/densmap/config.vsh.yaml @@ -6,7 +6,7 @@ description: | about the relative local density of the data. It is performed on the same inputs as UMAP. authors: - __merge__: /src/authors/jakub_majercik.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/dimred/pca/config.vsh.yaml b/src/dimred/pca/config.vsh.yaml index 9449dc89097..f6aef6e3d26 100644 --- a/src/dimred/pca/config.vsh.yaml +++ b/src/dimred/pca/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Computes PCA coordinates, loadings and variance decomposition. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: inputs arguments: diff --git a/src/dimred/tsne/config.vsh.yaml b/src/dimred/tsne/config.vsh.yaml index 261848b7bab..6717b0fe596 100644 --- a/src/dimred/tsne/config.vsh.yaml +++ b/src/dimred/tsne/config.vsh.yaml @@ -5,7 +5,7 @@ description: | t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality reduction technique used to visualize high-dimensional data in a low-dimensional space, revealing patterns and clusters by preserving local data similarities. authors: - __merge__: /src/authors/jakub_majercik.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/dimred/umap/config.vsh.yaml b/src/dimred/umap/config.vsh.yaml index 1b4b82a9504..8c12d8305f1 100644 --- a/src/dimred/umap/config.vsh.yaml +++ b/src/dimred/umap/config.vsh.yaml @@ -5,7 +5,7 @@ description: | UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/download/download_file/config.vsh.yaml b/src/download/download_file/config.vsh.yaml index aaeaf5dadf9..f71d2dd4c9f 100644 --- a/src/download/download_file/config.vsh.yaml +++ b/src/download/download_file/config.vsh.yaml @@ -10,7 +10,7 @@ usage: | --output output_rna.h5 authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" type: string diff --git a/src/download/sync_test_resources/config.vsh.yaml b/src/download/sync_test_resources/config.vsh.yaml index 8c88ad31e8b..5d01986cd0c 100644 --- a/src/download/sync_test_resources/config.vsh.yaml +++ b/src/download/sync_test_resources/config.vsh.yaml @@ -7,7 +7,7 @@ usage: | sync_test_resources --input _viash.yaml --output . authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/feature_annotation/align_query_reference/config.vsh.yaml b/src/feature_annotation/align_query_reference/config.vsh.yaml index 03bb5d73fb0..d19a929c80f 100644 --- a/src/feature_annotation/align_query_reference/config.vsh.yaml +++ b/src/feature_annotation/align_query_reference/config.vsh.yaml @@ -12,7 +12,7 @@ description: | authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml b/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml index 9ea3df8cae1..7ac1f307f4d 100644 --- a/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml +++ b/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml @@ -15,7 +15,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ contributor ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, contributor ] + roles: [ author, contributor ] arguments: # input - name: "--input" diff --git a/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml index 22cb0e8c2a1..321ad3dbcaf 100644 --- a/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml +++ b/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml @@ -6,8 +6,6 @@ authors: roles: [ author ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] description: | Calculates the score associated to S phase and G2M phase and annotates the cell cycle phase for each cell, as implemented by scanpy. diff --git a/src/feature_annotation/score_genes_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_scanpy/config.vsh.yaml index 508674049ad..fa8764554a0 100644 --- a/src/feature_annotation/score_genes_scanpy/config.vsh.yaml +++ b/src/feature_annotation/score_genes_scanpy/config.vsh.yaml @@ -6,8 +6,6 @@ authors: roles: [ author ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] description: | Calculates the score of a set of genes for each cell, as implemented by scanpy. diff --git a/src/files/make_params/config.vsh.yaml b/src/files/make_params/config.vsh.yaml index 5755a8802b3..2bed25f0ef0 100644 --- a/src/files/make_params/config.vsh.yaml +++ b/src/files/make_params/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, author ] + roles: [ author ] arguments: - name: "--base_dir" type: file diff --git a/src/filter/delimit_counts/config.vsh.yaml b/src/filter/delimit_counts/config.vsh.yaml index 399fb6c46b5..724fa14f242 100644 --- a/src/filter/delimit_counts/config.vsh.yaml +++ b/src/filter/delimit_counts/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Turns an .obs column containing count values into a boolean column based on thresholds. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/filter/delimit_fraction/config.vsh.yaml b/src/filter/delimit_fraction/config.vsh.yaml index f914582af34..b5084ed68c5 100644 --- a/src/filter/delimit_fraction/config.vsh.yaml +++ b/src/filter/delimit_fraction/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Turns a column containing values between 0 and 1 into a boolean column based on thresholds. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/filter/do_filter/config.vsh.yaml b/src/filter/do_filter/config.vsh.yaml index 2f0cd25e760..97cfec02bd9 100644 --- a/src/filter/do_filter/config.vsh.yaml +++ b/src/filter/do_filter/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Remove observations and variables based on specified .obs and .var columns. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, contributor ] + roles: [ contributor ] arguments: # input - name: "--input" diff --git a/src/filter/filter_with_counts/config.vsh.yaml b/src/filter/filter_with_counts/config.vsh.yaml index 5f0dabd97a1..06b7200acd9 100644 --- a/src/filter/filter_with_counts/config.vsh.yaml +++ b/src/filter/filter_with_counts/config.vsh.yaml @@ -9,7 +9,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, author ] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/filter/filter_with_scrublet/config.vsh.yaml b/src/filter/filter_with_scrublet/config.vsh.yaml index 085c7429d8a..c5f1a48df52 100644 --- a/src/filter/filter_with_scrublet/config.vsh.yaml +++ b/src/filter/filter_with_scrublet/config.vsh.yaml @@ -26,7 +26,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ contributor ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, contributor ] + roles: [ contributor ] arguments: # input - name: "--input" diff --git a/src/filter/intersect_obs/config.vsh.yaml b/src/filter/intersect_obs/config.vsh.yaml index dfdb3f66aa0..955eb6d8baa 100644 --- a/src/filter/intersect_obs/config.vsh.yaml +++ b/src/filter/intersect_obs/config.vsh.yaml @@ -7,7 +7,7 @@ description: | This component removes any observations which are not present in all modalities. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/isabelle_bergiers.yaml roles: [ contributor ] arguments: diff --git a/src/filter/remove_modality/config.vsh.yaml b/src/filter/remove_modality/config.vsh.yaml index bb87e7afa40..e06b2f7a398 100644 --- a/src/filter/remove_modality/config.vsh.yaml +++ b/src/filter/remove_modality/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Remove a modality from a .h5mu file authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" type: file diff --git a/src/filter/subset_h5mu/config.vsh.yaml b/src/filter/subset_h5mu/config.vsh.yaml index 60ff23d9283..70ab8d74bc2 100644 --- a/src/filter/subset_h5mu/config.vsh.yaml +++ b/src/filter/subset_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Create a subset of a mudata file by selecting the first number of observations authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" type: file diff --git a/src/filter/subset_obsp/config.vsh.yaml b/src/filter/subset_obsp/config.vsh.yaml index 38667bdebdb..46634c5b721 100644 --- a/src/filter/subset_obsp/config.vsh.yaml +++ b/src/filter/subset_obsp/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input arguments: diff --git a/src/integrate/harmony/config.vsh.yaml b/src/integrate/harmony/config.vsh.yaml index 62f072a3b8b..c8f15652785 100644 --- a/src/integrate/harmony/config.vsh.yaml +++ b/src/integrate/harmony/config.vsh.yaml @@ -7,7 +7,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, author ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/integrate/harmonypy/config.vsh.yaml b/src/integrate/harmonypy/config.vsh.yaml index e3c374e0b6f..72c466edd94 100644 --- a/src/integrate/harmonypy/config.vsh.yaml +++ b/src/integrate/harmonypy/config.vsh.yaml @@ -5,7 +5,7 @@ description: "Performs Harmony integration based as described in https://github. Based on an implementation in python from https://github.com/slowkow/harmonypy" authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor ] arguments: diff --git a/src/integrate/scanorama/config.vsh.yaml b/src/integrate/scanorama/config.vsh.yaml index 4a3b7c62ccc..3357b5f62d2 100644 --- a/src/integrate/scanorama/config.vsh.yaml +++ b/src/integrate/scanorama/config.vsh.yaml @@ -7,7 +7,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: [-i] diff --git a/src/integrate/scarches/config.vsh.yaml b/src/integrate/scarches/config.vsh.yaml index 4ec93176403..e0887db86df 100644 --- a/src/integrate/scarches/config.vsh.yaml +++ b/src/integrate/scarches/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/vladimir_shitov.yaml roles: [ author ] - __merge__: /src/authors/dorien_roosen.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs description: Arguments related to the input (query) dataset diff --git a/src/integrate/scvi/config.vsh.yaml b/src/integrate/scvi/config.vsh.yaml index df9508032cf..4027891a2a9 100644 --- a/src/integrate/scvi/config.vsh.yaml +++ b/src/integrate/scvi/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/malte_luecken.yaml roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/matthias_beyens.yaml roles: [ contributor ] argument_groups: diff --git a/src/integrate/totalvi/config.vsh.yaml b/src/integrate/totalvi/config.vsh.yaml index 6b782e614c8..ee8211718a5 100644 --- a/src/integrate/totalvi/config.vsh.yaml +++ b/src/integrate/totalvi/config.vsh.yaml @@ -7,9 +7,7 @@ info: documentation: https://docs.scvi-tools.org/en/1.3.2/tutorials/notebooks/multimodal/cite_scrna_integration_w_totalVI.html authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/labels_transfer/knn/config.vsh.yaml b/src/labels_transfer/knn/config.vsh.yaml index b785540ac4a..20a4c788268 100644 --- a/src/labels_transfer/knn/config.vsh.yaml +++ b/src/labels_transfer/knn/config.vsh.yaml @@ -5,7 +5,7 @@ description: | This component performs label transfer from reference to query using a K-Neirest Neighbors classifier. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ maintainer, author ] + roles: [ author ] - __merge__: /src/authors/vladimir_shitov.yaml roles: [ author ] diff --git a/src/mapping/bd_rhapsody/config.vsh.yaml b/src/mapping/bd_rhapsody/config.vsh.yaml index cef897041d3..bf475fb8b91 100644 --- a/src/mapping/bd_rhapsody/config.vsh.yaml +++ b/src/mapping/bd_rhapsody/config.vsh.yaml @@ -18,9 +18,7 @@ info: license: Unknown authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/mapping/cellranger_count/config.vsh.yaml b/src/mapping/cellranger_count/config.vsh.yaml index ef2a3eafad0..9f82e8a7996 100644 --- a/src/mapping/cellranger_count/config.vsh.yaml +++ b/src/mapping/cellranger_count/config.vsh.yaml @@ -8,7 +8,7 @@ authors: - __merge__: /src/authors/samuel_d_souza.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/mapping/cellranger_count_split/config.vsh.yaml b/src/mapping/cellranger_count_split/config.vsh.yaml index 1db809f67e0..b871c94b6a7 100644 --- a/src/mapping/cellranger_count_split/config.vsh.yaml +++ b/src/mapping/cellranger_count_split/config.vsh.yaml @@ -8,7 +8,7 @@ authors: - __merge__: /src/authors/samuel_d_souza.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: - name: --input type: file diff --git a/src/mapping/cellranger_multi/config.vsh.yaml b/src/mapping/cellranger_multi/config.vsh.yaml index 418c6bae414..f8483ffaede 100644 --- a/src/mapping/cellranger_multi/config.vsh.yaml +++ b/src/mapping/cellranger_multi/config.vsh.yaml @@ -4,15 +4,13 @@ scope: "public" description: Align fastq files using Cell Ranger multi. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] __merge__: /src/mapping/cellranger_multi/cellranger_multi.yaml diff --git a/src/mapping/htseq_count/config.vsh.yaml b/src/mapping/htseq_count/config.vsh.yaml index b20468d8512..176e8ae2e40 100644 --- a/src/mapping/htseq_count/config.vsh.yaml +++ b/src/mapping/htseq_count/config.vsh.yaml @@ -9,7 +9,7 @@ description: | See http://htseq.readthedocs.io/en/master/count.html for details. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] argument_groups: diff --git a/src/mapping/htseq_count_to_h5mu/config.vsh.yaml b/src/mapping/htseq_count_to_h5mu/config.vsh.yaml index f3fe174e06b..67bdd384b75 100644 --- a/src/mapping/htseq_count_to_h5mu/config.vsh.yaml +++ b/src/mapping/htseq_count_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Convert the htseq table to a h5mu. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] argument_groups: diff --git a/src/mapping/multi_star/config.vsh.yaml b/src/mapping/multi_star/config.vsh.yaml index 25b4f11fc85..2f142a4aa33 100644 --- a/src/mapping/multi_star/config.vsh.yaml +++ b/src/mapping/multi_star/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] # generated the argument groups using `utils/process_params.R` __merge__: [., arguments_star.yaml, arguments_htseq.yaml] # manually taking care of the main input files diff --git a/src/mapping/multi_star_to_h5mu/config.vsh.yaml b/src/mapping/multi_star_to_h5mu/config.vsh.yaml index a9f2280c314..e12185ef1e9 100644 --- a/src/mapping/multi_star_to_h5mu/config.vsh.yaml +++ b/src/mapping/multi_star_to_h5mu/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Convert the output of `multi_star` to a h5mu. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] arguments: diff --git a/src/mapping/samtools_sort/config.vsh.yaml b/src/mapping/samtools_sort/config.vsh.yaml index 0d35015fff5..50c97561d28 100644 --- a/src/mapping/samtools_sort/config.vsh.yaml +++ b/src/mapping/samtools_sort/config.vsh.yaml @@ -13,7 +13,7 @@ description: | Thus the `--sort_by_read_names` and `--sort_by ` options are incompatible with `--output_bai`. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] argument_groups: diff --git a/src/mapping/star_align/config.vsh.yaml b/src/mapping/star_align/config.vsh.yaml index 7930906d510..736425aa381 100644 --- a/src/mapping/star_align/config.vsh.yaml +++ b/src/mapping/star_align/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] # generated the argument groups using `utils/process_params.R` __merge__: [., argument_groups.yaml] # manually taking care of the main input files diff --git a/src/mapping/star_align_v273a/config.vsh.yaml b/src/mapping/star_align_v273a/config.vsh.yaml index 4602604bd40..0c3ee4773a4 100644 --- a/src/mapping/star_align_v273a/config.vsh.yaml +++ b/src/mapping/star_align_v273a/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] # as long as argument_groups.yaml is the same between both versions, just use that __merge__: [., ../star_align/argument_groups.yaml] # __merge__: [., argument_groups.yaml] diff --git a/src/metadata/add_id/config.vsh.yaml b/src/metadata/add_id/config.vsh.yaml index 07873366e91..1203d090c9e 100644 --- a/src/metadata/add_id/config.vsh.yaml +++ b/src/metadata/add_id/config.vsh.yaml @@ -6,7 +6,7 @@ description: | by prefixing the values with an unique id per .h5mu file. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/metadata/grep_annotation_column/config.vsh.yaml b/src/metadata/grep_annotation_column/config.vsh.yaml index 6a2a8ded6dd..cb0e6c7adbf 100644 --- a/src/metadata/grep_annotation_column/config.vsh.yaml +++ b/src/metadata/grep_annotation_column/config.vsh.yaml @@ -6,7 +6,7 @@ description: | The annotation matrix can originate from either a modality, or all modalities (global .var or .obs). authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs description: Arguments related to the input dataset. diff --git a/src/neighbors/bbknn/config.vsh.yaml b/src/neighbors/bbknn/config.vsh.yaml index 6ae8b8d5985..41b3bc2ed11 100644 --- a/src/neighbors/bbknn/config.vsh.yaml +++ b/src/neighbors/bbknn/config.vsh.yaml @@ -7,7 +7,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: # inputs - name: "--input" diff --git a/src/neighbors/find_neighbors/config.vsh.yaml b/src/neighbors/find_neighbors/config.vsh.yaml index fd6bd43a8c7..be143267947 100644 --- a/src/neighbors/find_neighbors/config.vsh.yaml +++ b/src/neighbors/find_neighbors/config.vsh.yaml @@ -7,7 +7,7 @@ description: | The neighbor search efficiency of this heavily relies on UMAP [McInnes18], which also provides a method for estimating connectivities of data points - the connectivity of the manifold (method=='umap'). If method=='gauss', connectivities are computed according to [Coifman05], in the adaption of [Haghverdi16]. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor ] arguments: diff --git a/src/process_10xh5/filter_10xh5/config.vsh.yaml b/src/process_10xh5/filter_10xh5/config.vsh.yaml index 9e0e6a980da..dc14422cf94 100644 --- a/src/process_10xh5/filter_10xh5/config.vsh.yaml +++ b/src/process_10xh5/filter_10xh5/config.vsh.yaml @@ -10,7 +10,7 @@ usage: | --min_library_size 1000 --min_cells_per_gene 300 authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" type: file diff --git a/src/query/cellxgene_census/config.vsh.yaml b/src/query/cellxgene_census/config.vsh.yaml index 0790e71dd59..c138c9f48b6 100644 --- a/src/query/cellxgene_census/config.vsh.yaml +++ b/src/query/cellxgene_census/config.vsh.yaml @@ -8,7 +8,7 @@ description: | the dataset metadata and joins it into the cell metadata. authors: - __merge__: /src/authors/matthias_beyens.yaml - roles: [ maintainer, author ] + roles: [ author ] - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml diff --git a/src/query/tiledb_soma_healthcheck/config.vsh.yaml b/src/query/tiledb_soma_healthcheck/config.vsh.yaml index 8541b50372e..6c00439377e 100644 --- a/src/query/tiledb_soma_healthcheck/config.vsh.yaml +++ b/src/query/tiledb_soma_healthcheck/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Checks if a provided location can be queried as a TileDB-SOMA database. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input database description: "Open a TileDB SOMA database by URI." diff --git a/src/reference/build_bdrhap_reference/config.vsh.yaml b/src/reference/build_bdrhap_reference/config.vsh.yaml index 7d345321bc4..3118da650f3 100644 --- a/src/reference/build_bdrhap_reference/config.vsh.yaml +++ b/src/reference/build_bdrhap_reference/config.vsh.yaml @@ -12,9 +12,7 @@ description: | - Filtered GTF file authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/reference/build_cellranger_reference/config.vsh.yaml b/src/reference/build_cellranger_reference/config.vsh.yaml index 7d13a07a267..7d2177fe7f0 100644 --- a/src/reference/build_cellranger_reference/config.vsh.yaml +++ b/src/reference/build_cellranger_reference/config.vsh.yaml @@ -6,7 +6,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: # inputs - type: file diff --git a/src/reference/make_reference/config.vsh.yaml b/src/reference/make_reference/config.vsh.yaml index 35199d3ee90..c067525c12b 100644 --- a/src/reference/make_reference/config.vsh.yaml +++ b/src/reference/make_reference/config.vsh.yaml @@ -12,7 +12,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] arguments: # inputs - type: file diff --git a/src/report/mermaid/config.vsh.yaml b/src/report/mermaid/config.vsh.yaml index b04add17386..e60298b96b0 100644 --- a/src/report/mermaid/config.vsh.yaml +++ b/src/report/mermaid/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Generates a network from mermaid code. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" diff --git a/src/tiledb/move_mudata_obs_to_tiledb/config.vsh.yaml b/src/tiledb/move_mudata_obs_to_tiledb/config.vsh.yaml index 666ec6dc75b..d3058a2b35d 100644 --- a/src/tiledb/move_mudata_obs_to_tiledb/config.vsh.yaml +++ b/src/tiledb/move_mudata_obs_to_tiledb/config.vsh.yaml @@ -7,7 +7,7 @@ description: | their order should match with what is already present the tiledb database. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input database description: "Open a tileDB-SOMA database by URI or as a local directory." diff --git a/src/tiledb/move_mudata_obsm_to_tiledb/config.vsh.yaml b/src/tiledb/move_mudata_obsm_to_tiledb/config.vsh.yaml index 0697bb297f7..acdf335399a 100644 --- a/src/tiledb/move_mudata_obsm_to_tiledb/config.vsh.yaml +++ b/src/tiledb/move_mudata_obsm_to_tiledb/config.vsh.yaml @@ -7,7 +7,7 @@ description: | their order should match with what is already present the tiledb database. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input database description: "Open a tileDB-SOMA database by URI." diff --git a/src/tiledb/move_mudata_obsp_to_tiledb/config.vsh.yaml b/src/tiledb/move_mudata_obsp_to_tiledb/config.vsh.yaml index 8b3fb1c0df8..c35f4a9dfeb 100644 --- a/src/tiledb/move_mudata_obsp_to_tiledb/config.vsh.yaml +++ b/src/tiledb/move_mudata_obsp_to_tiledb/config.vsh.yaml @@ -7,7 +7,7 @@ description: | their order should match with what is already present the tiledb database. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Input database description: "Open a tileDB-SOMA database by URI." diff --git a/src/transform/bpcells_regress_out/config.vsh.yaml b/src/transform/bpcells_regress_out/config.vsh.yaml index f476924c189..ef479b1d167 100644 --- a/src/transform/bpcells_regress_out/config.vsh.yaml +++ b/src/transform/bpcells_regress_out/config.vsh.yaml @@ -5,11 +5,10 @@ description: | Regress out the effects of confounding variables using a linear least squares regression model with BPCells. authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ maintainer, author ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor, author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + arguments: - name: "--input" type: file diff --git a/src/transform/clr/config.vsh.yaml b/src/transform/clr/config.vsh.yaml index cff0a8987b6..9669c420c0c 100644 --- a/src/transform/clr/config.vsh.yaml +++ b/src/transform/clr/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017). authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/transform/delete_layer/config.vsh.yaml b/src/transform/delete_layer/config.vsh.yaml index 2a380993683..aac7e602b33 100644 --- a/src/transform/delete_layer/config.vsh.yaml +++ b/src/transform/delete_layer/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Delete an anndata layer from one or more modalities. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/transform/log1p/config.vsh.yaml b/src/transform/log1p/config.vsh.yaml index 44eb53682b4..0512f8756f5 100644 --- a/src/transform/log1p/config.vsh.yaml +++ b/src/transform/log1p/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor ] arguments: diff --git a/src/transform/normalize_total/config.vsh.yaml b/src/transform/normalize_total/config.vsh.yaml index 123be005c3e..44ba99cd51b 100644 --- a/src/transform/normalize_total/config.vsh.yaml +++ b/src/transform/normalize_total/config.vsh.yaml @@ -9,7 +9,7 @@ description: | If exclude_highly_expressed=True, very highly expressed genes are excluded from the computation of the normalization factor (size factor) for each cell. This is meaningful as these can strongly influence the resulting normalized values for all other genes [Weinreb17]. authors: - __merge__: /src/authors/dries_de_maeyer.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ contributor ] arguments: diff --git a/src/transform/regress_out/config.vsh.yaml b/src/transform/regress_out/config.vsh.yaml index b8cb814efaa..168c38f7666 100644 --- a/src/transform/regress_out/config.vsh.yaml +++ b/src/transform/regress_out/config.vsh.yaml @@ -8,7 +8,7 @@ description: | See https://github.com/theislab/scanpy/issues/526. authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer, contributor ] + roles: [ author, contributor ] arguments: - name: "--input" type: file diff --git a/src/transform/scale/config.vsh.yaml b/src/transform/scale/config.vsh.yaml index 792f13b52d3..d1431c14aec 100644 --- a/src/transform/scale/config.vsh.yaml +++ b/src/transform/scale/config.vsh.yaml @@ -5,7 +5,7 @@ description: | Scale data to unit variance and zero mean. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] arguments: # input - name: "--input" diff --git a/src/transform/tfidf/config.vsh.yaml b/src/transform/tfidf/config.vsh.yaml index 72615314e65..7071d2e8042 100644 --- a/src/transform/tfidf/config.vsh.yaml +++ b/src/transform/tfidf/config.vsh.yaml @@ -10,7 +10,7 @@ description: | across different cells while down-weighting regions that are commonly accessible across many cells. authors: - __merge__: /src/authors/vladimir_shitov.yaml - roles: [ maintainer ] + roles: [ author ] arguments: # input - name: "--input" diff --git a/src/velocity/scvelo/config.vsh.yaml b/src/velocity/scvelo/config.vsh.yaml index 7b263f3fb68..5c92a4189d3 100644 --- a/src/velocity/scvelo/config.vsh.yaml +++ b/src/velocity/scvelo/config.vsh.yaml @@ -3,7 +3,7 @@ namespace: "velocity" scope: "public" authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/velocity/velocyto/config.vsh.yaml b/src/velocity/velocyto/config.vsh.yaml index 7bfad72a395..38fd898bb61 100644 --- a/src/velocity/velocyto/config.vsh.yaml +++ b/src/velocity/velocyto/config.vsh.yaml @@ -4,7 +4,7 @@ scope: "public" description: "Runs the velocity analysis on a BAM file, outputting a loom file." authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] arguments: - name: "--input" alternatives: [-i] diff --git a/src/velocity/velocyto_to_h5mu/config.vsh.yaml b/src/velocity/velocyto_to_h5mu/config.vsh.yaml index 9aad3a982ad..1b71234a956 100644 --- a/src/velocity/velocyto_to_h5mu/config.vsh.yaml +++ b/src/velocity/velocyto_to_h5mu/config.vsh.yaml @@ -8,7 +8,7 @@ description: | h5ad object will get added to that h5mu instead. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ maintainer, author ] + roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml diff --git a/src/workflows/annotation/celltypist/config.vsh.yaml b/src/workflows/annotation/celltypist/config.vsh.yaml index 4354170c316..dff4838b1bd 100644 --- a/src/workflows/annotation/celltypist/config.vsh.yaml +++ b/src/workflows/annotation/celltypist/config.vsh.yaml @@ -9,9 +9,7 @@ info: namespace: test_workflows/annotation authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Inputs diff --git a/src/workflows/annotation/harmony_knn/config.vsh.yaml b/src/workflows/annotation/harmony_knn/config.vsh.yaml index 126cd62d121..e0fc3e3a256 100644 --- a/src/workflows/annotation/harmony_knn/config.vsh.yaml +++ b/src/workflows/annotation/harmony_knn/config.vsh.yaml @@ -9,9 +9,7 @@ info: namespace: test_workflows/annotation authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Query Input diff --git a/src/workflows/annotation/scanvi_scarches/config.vsh.yaml b/src/workflows/annotation/scanvi_scarches/config.vsh.yaml index 0f05efb628c..4a20750b14b 100644 --- a/src/workflows/annotation/scanvi_scarches/config.vsh.yaml +++ b/src/workflows/annotation/scanvi_scarches/config.vsh.yaml @@ -4,9 +4,7 @@ scope: "public" description: "Cell type annotation workflow using ScanVI with scArches for reference mapping." authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] info: name: "scANVI - scArches workflow" diff --git a/src/workflows/annotation/scvi_knn/config.vsh.yaml b/src/workflows/annotation/scvi_knn/config.vsh.yaml index c4ba039c075..90e7578c626 100644 --- a/src/workflows/annotation/scvi_knn/config.vsh.yaml +++ b/src/workflows/annotation/scvi_knn/config.vsh.yaml @@ -8,9 +8,7 @@ description: | The workflow does not currently output the trained SCVI reference model." authors: - __merge__: /src/authors/dorien_roosen.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] info: name: "scVI Annotation" test_dependencies: diff --git a/src/workflows/differential_expression/pseudobulk_deseq2/config.vsh.yaml b/src/workflows/differential_expression/pseudobulk_deseq2/config.vsh.yaml index a4603a1a34d..3dba97f82ce 100644 --- a/src/workflows/differential_expression/pseudobulk_deseq2/config.vsh.yaml +++ b/src/workflows/differential_expression/pseudobulk_deseq2/config.vsh.yaml @@ -6,8 +6,6 @@ description: | authors: - __merge__: /src/authors/jakub_majercik.yaml roles: [ author ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] info: test_dependencies: - name: pseudobulk_deseq2_test diff --git a/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml b/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml index 627794bd0f9..27bc618cb9a 100644 --- a/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml +++ b/src/workflows/ingestion/bd_rhapsody/config.vsh.yaml @@ -18,7 +18,7 @@ description: | authors: - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ maintainer ] + roles: [ author ] - __merge__: /src/authors/dorien_roosen.yaml roles: [ author ] diff --git a/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml b/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml index ed7c015ee74..4551228805a 100644 --- a/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml +++ b/src/workflows/ingestion/cellranger_mapping/config.vsh.yaml @@ -11,7 +11,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] argument_groups: diff --git a/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml b/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml index f6f7be866c5..9faf8854d2e 100644 --- a/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml +++ b/src/workflows/ingestion/cellranger_postprocessing/config.vsh.yaml @@ -13,7 +13,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/workflows/ingestion/conversion/config.vsh.yaml b/src/workflows/ingestion/conversion/config.vsh.yaml index 6afaa14addd..eb4169ff3c7 100644 --- a/src/workflows/ingestion/conversion/config.vsh.yaml +++ b/src/workflows/ingestion/conversion/config.vsh.yaml @@ -9,7 +9,7 @@ info: namespace: test_workflows/ingestion authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] argument_groups: diff --git a/src/workflows/ingestion/demux/config.vsh.yaml b/src/workflows/ingestion/demux/config.vsh.yaml index 69d10bfe9f6..7667f31805c 100644 --- a/src/workflows/ingestion/demux/config.vsh.yaml +++ b/src/workflows/ingestion/demux/config.vsh.yaml @@ -9,7 +9,7 @@ info: test_dependencies: authors: - __merge__: /src/authors/toni_verbeiren.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/marijke_van_moerbeke.yaml roles: [ author ] - __merge__: /src/authors/angela_pisco.yaml diff --git a/src/workflows/ingestion/make_reference/config.vsh.yaml b/src/workflows/ingestion/make_reference/config.vsh.yaml index 465ebdca845..6b1585b4782 100644 --- a/src/workflows/ingestion/make_reference/config.vsh.yaml +++ b/src/workflows/ingestion/make_reference/config.vsh.yaml @@ -9,9 +9,7 @@ authors: - __merge__: /src/authors/angela_pisco.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] - - __merge__: /src/authors/weiwei_schultz.yaml - roles: [ contributor ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/workflows/multiomics/process_batches/config.vsh.yaml b/src/workflows/multiomics/process_batches/config.vsh.yaml index 4d09483d131..0eb554c7f25 100644 --- a/src/workflows/multiomics/process_batches/config.vsh.yaml +++ b/src/workflows/multiomics/process_batches/config.vsh.yaml @@ -9,7 +9,7 @@ description: | assumes that samples from multiple pipelines are already concatenated. authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] info: test_dependencies: - name: workflow_test diff --git a/src/workflows/multiomics/process_samples/config.vsh.yaml b/src/workflows/multiomics/process_samples/config.vsh.yaml index 224a4466d44..3e67cbb95cc 100644 --- a/src/workflows/multiomics/process_samples/config.vsh.yaml +++ b/src/workflows/multiomics/process_samples/config.vsh.yaml @@ -16,7 +16,7 @@ info: namespace: test_workflows/multiomics/process_samples authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] argument_groups: - name: Inputs arguments: diff --git a/src/workflows/multiomics/split_h5mu/config.vsh.yaml b/src/workflows/multiomics/split_h5mu/config.vsh.yaml index d5b0ef1f986..3f8771cac67 100644 --- a/src/workflows/multiomics/split_h5mu/config.vsh.yaml +++ b/src/workflows/multiomics/split_h5mu/config.vsh.yaml @@ -4,7 +4,7 @@ scope: "private" description: "Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. " authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] info: test_dependencies: - name: split_h5mu_test diff --git a/src/workflows/multiomics/split_modalities/config.vsh.yaml b/src/workflows/multiomics/split_modalities/config.vsh.yaml index 196dacf5a46..69f475a5667 100644 --- a/src/workflows/multiomics/split_modalities/config.vsh.yaml +++ b/src/workflows/multiomics/split_modalities/config.vsh.yaml @@ -4,7 +4,7 @@ scope: "private" description: "A pipeline to split a multimodal mudata files into several unimodal mudata files." authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] info: test_dependencies: - name: split_modalities_test diff --git a/src/workflows/prot/prot_singlesample/config.vsh.yaml b/src/workflows/prot/prot_singlesample/config.vsh.yaml index 5b31e9c8093..8222a2bbf57 100644 --- a/src/workflows/prot/prot_singlesample/config.vsh.yaml +++ b/src/workflows/prot/prot_singlesample/config.vsh.yaml @@ -9,7 +9,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml roles: [ author ] argument_groups: diff --git a/src/workflows/qc/qc/config.vsh.yaml b/src/workflows/qc/qc/config.vsh.yaml index c1bbe46ebad..2167d379e26 100644 --- a/src/workflows/qc/qc/config.vsh.yaml +++ b/src/workflows/qc/qc/config.vsh.yaml @@ -4,7 +4,7 @@ scope: "public" description: "A pipeline to add basic qc statistics to a MuData " authors: - __merge__: /src/authors/dries_schaumont.yaml - roles: [ author, maintainer ] + roles: [ author ] info: test_dependencies: - name: qc_test diff --git a/src/workflows/rna/rna_multisample/config.vsh.yaml b/src/workflows/rna/rna_multisample/config.vsh.yaml index d3b6ceb56d3..cc592d220da 100644 --- a/src/workflows/rna/rna_multisample/config.vsh.yaml +++ b/src/workflows/rna/rna_multisample/config.vsh.yaml @@ -9,7 +9,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml roles: [ author ] argument_groups: diff --git a/src/workflows/rna/rna_singlesample/config.vsh.yaml b/src/workflows/rna/rna_singlesample/config.vsh.yaml index 1a8c51ea63d..c1e37a6757e 100644 --- a/src/workflows/rna/rna_singlesample/config.vsh.yaml +++ b/src/workflows/rna/rna_singlesample/config.vsh.yaml @@ -9,7 +9,7 @@ authors: - __merge__: /src/authors/dries_de_maeyer.yaml roles: [ author ] - __merge__: /src/authors/robrecht_cannoodt.yaml - roles: [ author, maintainer ] + roles: [ author ] - __merge__: /src/authors/dries_schaumont.yaml roles: [ author ] argument_groups: