From 2ff37a4e472f05b036da98e93e8e518b8f6382e6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 08:56:01 +0200 Subject: [PATCH 1/7] fix render_readme crashing on comp_process_integration * use relative __merge__ paths in comp_process_integration.yaml, the leading slash made the newer render_readme choke looking for /src/api/file_dataset.yaml on disk * drop --input src/api from create_readme.sh, create_task_readme no longer takes it * bump common submodule * regenerate readme --- CHANGELOG.md | 1 + README.md | 122 +++++++++++++------------- common | 2 +- scripts/create_readme.sh | 2 +- src/api/comp_process_integration.yaml | 4 +- 5 files changed, 66 insertions(+), 65 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 794c5618f..e28ea5a75 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,6 +34,7 @@ * Update scPRINT to use latest stable version (PR #70) * Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78). +* Fix `render_readme` crashing on `comp_process_integration.yaml`'s absolute `__merge__` paths. * Split Scanorama into two methods/scores - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. diff --git a/README.md b/README.md index 7fab7a52a..e46ee430d 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ aim to remove batch effects scRNA-seq datasets \[@zappia2018exploring\]. These methods balance the removal of batch effects with the conservation of nuanced biological information in different ways. This abundance of tools has complicated batch integration method choice, leading to -several benchmarks on this topic \[@luecken2020benchmarking; +several benchmarks on this topic \[@luecken2022benchmarking; @tran2020benchmark; @chazarragil2021flexible; @mereu2020benchmarking\]. Yet, benchmarks use different metrics, method implementations and datasets. Here we build a living benchmarking task for batch integration @@ -46,15 +46,18 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| name | roles | -|:------------------|:-------------------| -| Michaela Mueller | maintainer, author | -| Malte Luecken | author | -| Daniel Strobl | author | -| Robrecht Cannoodt | contributor | -| Scott Gigante | contributor | -| Kai Waldrant | contributor | -| Nartin Kim | contributor | +| Name | Roles | Orcid | Github | +|:------------------|:-------------------|:--------------------|:-------------| +| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | +| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | +| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | +| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | +| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | +| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | +| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | +| Martin Kim | contributor | 0009-0003-8555-1361 | martinkim0 | +| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | +| Jeremie Kalfon | contributor | 0000-0002-2818-9728 | jkobject | ## API @@ -64,27 +67,27 @@ flowchart TB comp_process_dataset[/"Data processor"/] file_dataset("Dataset") file_solution("Solution") - comp_control_method[/"Control method"/] comp_method[/"Method"/] - comp_process_integration[/"Process integration"/] - comp_metric[/"Metric"/] + comp_control_method[/"Control method"/] file_integrated("Integration") + comp_process_integration[/"Process integration"/] file_integrated_processed("Processed integration output") + comp_metric[/"Metric"/] file_score("Score") file_common_dataset---comp_process_dataset comp_process_dataset-->file_dataset comp_process_dataset-->file_solution - file_dataset---comp_control_method file_dataset---comp_method + file_dataset---comp_control_method file_dataset---comp_process_integration file_solution---comp_control_method file_solution---comp_metric - comp_control_method-->file_integrated comp_method-->file_integrated - comp_process_integration-->file_integrated_processed - comp_metric-->file_score + comp_control_method-->file_integrated file_integrated---comp_process_integration + comp_process_integration-->file_integrated_processed file_integrated_processed---comp_metric + comp_metric-->file_score ``` ## File format: Common Dataset @@ -149,7 +152,7 @@ Arguments: | `--input` | `file` | A subset of the common dataset. | | `--output_dataset` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | | `--output_solution` | `file` | (*Output*) Uncensored dataset containing the true labels. | -| `--hvgs` | `integer` | (*Optional*) NA. Default: `2000`. | +| `--hvgs` | `integer` | (*Optional*) Subset the count matrix to this number of HVGs. Default: `2000`. | @@ -249,22 +252,6 @@ Data structure: -## Component type: Control method - -A control method for the batch integration task. - -Arguments: - -
- -| Name | Type | Description | -|:-------------------|:-------|:-----------------------------------------------| -| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | -| `--input_solution` | `file` | Uncensored dataset containing the true labels. | -| `--output` | `file` | (*Output*) An integrated AnnData dataset. | - -
- ## Component type: Method A method for the batch integration task. @@ -280,39 +267,19 @@ Arguments: -## Component type: Process integration - -Process output from an integration method to the format expected by -metrics - -Arguments: - -
- -| Name | Type | Description | -|:---|:---|:---| -| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | -| `--input_integrated` | `file` | An integrated AnnData dataset. | -| `--expected_method_types` | `string` | NA. | -| `--expected_method_types` | `string` | NA. | -| `--expected_method_types` | `string` | NA. | -| `--output` | `file` | (*Output*) An integrated AnnData dataset with additional outputs. | - -
- -## Component type: Metric +## Component type: Control method -A metric for evaluating batch integration methods. +A control method for the batch integration task. Arguments:
-| Name | Type | Description | -|:---|:---|:---| -| `--input_integrated` | `file` | An integrated AnnData dataset with additional outputs. | +| Name | Type | Description | +|:-------------------|:-------|:-----------------------------------------------| +| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | | `--input_solution` | `file` | Uncensored dataset containing the true labels. | -| `--output` | `file` | (*Output*) Metric score file. | +| `--output` | `file` | (*Output*) An integrated AnnData dataset. |
@@ -361,6 +328,24 @@ Data structure: +## Component type: Process integration + +Process output from an integration method to the format expected by +metrics + +Arguments: + +
+ +| Name | Type | Description | +|:---|:---|:---| +| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | +| `--input_integrated` | `file` | An integrated AnnData dataset. | +| `--expected_method_types` | `string` | The expected output types of the batch integration method. | +| `--output` | `file` | (*Output*) An integrated AnnData dataset with additional outputs. | + +
+ ## File format: Processed integration output An integrated AnnData dataset with additional outputs. @@ -410,6 +395,22 @@ Data structure: +## Component type: Metric + +A metric for evaluating batch integration methods. + +Arguments: + +
+ +| Name | Type | Description | +|:---|:---|:---| +| `--input_integrated` | `file` | An integrated AnnData dataset with additional outputs. | +| `--input_solution` | `file` | Uncensored dataset containing the true labels. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ ## File format: Score Metric score file @@ -438,4 +439,3 @@ Data structure: | `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - diff --git a/common b/common index 67da19a36..deb906ef7 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 67da19a36ae56ea068804d15ccadec88a06da920 +Subproject commit deb906ef7abacf8809291631372c8aacadabeae9 diff --git a/scripts/create_readme.sh b/scripts/create_readme.sh index 0ed7aafe9..432aab468 100755 --- a/scripts/create_readme.sh +++ b/scripts/create_readme.sh @@ -2,4 +2,4 @@ set -e -common/scripts/create_task_readme --input src/api +common/scripts/create_task_readme diff --git a/src/api/comp_process_integration.yaml b/src/api/comp_process_integration.yaml index 944df29cf..e6162c012 100644 --- a/src/api/comp_process_integration.yaml +++ b/src/api/comp_process_integration.yaml @@ -14,12 +14,12 @@ argument_groups: - name: Inputs arguments: - name: "--input_dataset" - __merge__: /src/api/file_dataset.yaml + __merge__: file_dataset.yaml type: file direction: input required: true - name: "--input_integrated" - __merge__: /src/api/file_integrated.yaml + __merge__: file_integrated.yaml type: file direction: input required: true From 9c26aa27cbe3dc53a561bd097739ed4b3bb8092a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 09:26:59 +0200 Subject: [PATCH 2/7] credit missing contributors * add Seohyon Kim, Tianyu Liu, Josep Garnica, Calvin McCarter, Daniel Schaffer, Stephen Chung and Wendao Liu to the authors list * promote contributors with two or more merged PRs to author * drop Martin Kim's orcid, it was a copy of Kai Waldrant's * regenerate readme --- CHANGELOG.md | 2 +- README.md | 31 +++++++++++++++++++------------ _viash.yaml | 38 ++++++++++++++++++++++++++++++++++---- 3 files changed, 54 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e28ea5a75..8a64b2e73 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,12 +29,12 @@ * Un-pin the scPRINT version and update parameters (PR #51) * Update scPRINT to better handle large datasets, including a new default model (PR #54) +* Credit contributors missing from the authors list, and fix Martin Kim's orcid. ## Bug fixes * Update scPRINT to use latest stable version (PR #70) * Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78). -* Fix `render_readme` crashing on `comp_process_integration.yaml`'s absolute `__merge__` paths. * Split Scanorama into two methods/scores - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. diff --git a/README.md b/README.md index e46ee430d..6d316420f 100644 --- a/README.md +++ b/README.md @@ -46,18 +46,25 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| Name | Roles | Orcid | Github | -|:------------------|:-------------------|:--------------------|:-------------| -| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | -| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | -| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | -| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | -| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | -| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | -| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | -| Martin Kim | contributor | 0009-0003-8555-1361 | martinkim0 | -| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | -| Jeremie Kalfon | contributor | 0000-0002-2818-9728 | jkobject | +| Name | Roles | Orcid | Github | +|:------------------|:-------------------|:--------------------|:-----------------| +| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | +| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | +| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | +| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | +| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | +| Jeremie Kalfon | author | 0000-0002-2818-9728 | jkobject | +| Seohyon Kim | author | | seohyonkim | +| Josep Garnica | author | 0000-0001-9493-1321 | JGarnica22 | +| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | +| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | +| Martin Kim | contributor | | martinkim0 | +| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | +| Tianyu Liu | contributor | 0000-0002-9412-6573 | HelloWorldLTY | +| Calvin McCarter | contributor | 0000-0002-7257-1350 | calvinmccarter | +| Daniel Schaffer | contributor | | schafferde | +| Stephen Chung | contributor | | stephen-chung-mh | +| Wendao Liu | contributor | | liuwd15 | ## API diff --git a/_viash.yaml b/_viash.yaml index 626b71f88..762a9c641 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -71,6 +71,20 @@ authors: info: github: lazappi orcid: 0000-0001-7744-8565 + - name: Jeremie Kalfon + roles: [author] + info: + github: jkobject + orcid: 0000-0002-2818-9728 + - name: Seohyon Kim + roles: [author] + info: + github: seohyonkim + - name: Josep Garnica + roles: [author] + info: + github: JGarnica22 + orcid: 0000-0001-9493-1321 - name: "Scott Gigante" roles: [ contributor ] info: @@ -85,17 +99,33 @@ authors: roles: [ contributor ] info: github: martinkim0 - orcid: "0009-0003-8555-1361" - name: Sai Nirmayi Yasa roles: [contributor] info: github: sainirmayi orcid: 0009-0003-6319-9803 - - name: Jeremie Kalfon + - name: Tianyu Liu roles: [contributor] info: - github: jkobject - orcid: 0000-0002-2818-9728 + github: HelloWorldLTY + orcid: 0000-0002-9412-6573 + - name: Calvin McCarter + roles: [contributor] + info: + github: calvinmccarter + orcid: 0000-0002-7257-1350 + - name: Daniel Schaffer + roles: [contributor] + info: + github: schafferde + - name: Stephen Chung + roles: [contributor] + info: + github: stephen-chung-mh + - name: Wendao Liu + roles: [contributor] + info: + github: liuwd15 config_mods: | .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" } From 2789514e62ce363214480ed9dade35e579b043ba Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 09:40:21 +0200 Subject: [PATCH 3/7] Add orcid and fix name --- README.md | 38 +++++++++++++++++++------------------- _viash.yaml | 5 +++-- 2 files changed, 22 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 6d316420f..3ea4fca0e 100644 --- a/README.md +++ b/README.md @@ -46,25 +46,25 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| Name | Roles | Orcid | Github | -|:------------------|:-------------------|:--------------------|:-----------------| -| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | -| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | -| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | -| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | -| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | -| Jeremie Kalfon | author | 0000-0002-2818-9728 | jkobject | -| Seohyon Kim | author | | seohyonkim | -| Josep Garnica | author | 0000-0001-9493-1321 | JGarnica22 | -| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | -| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | -| Martin Kim | contributor | | martinkim0 | -| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | -| Tianyu Liu | contributor | 0000-0002-9412-6573 | HelloWorldLTY | -| Calvin McCarter | contributor | 0000-0002-7257-1350 | calvinmccarter | -| Daniel Schaffer | contributor | | schafferde | -| Stephen Chung | contributor | | stephen-chung-mh | -| Wendao Liu | contributor | | liuwd15 | +| Name | Roles | Github | Orcid | +|:------------------|:-------------------|:-----------------|:--------------------| +| Michaela Mueller | maintainer, author | mumichae | 0000-0002-1401-1785 | +| Malte Luecken | author | LuckyMD | 0000-0001-7464-7921 | +| Daniel Strobl | author | danielStrobl | 0000-0002-5516-7057 | +| Robrecht Cannoodt | author | rcannood | 0000-0003-3641-729X | +| Luke Zappia | author | lazappi | 0000-0001-7744-8565 | +| Jeremie Kalfon | author | jkobject | 0000-0002-2818-9728 | +| Seo Hyon Kim | author | seohyonkim | 0009-0007-3062-4681 | +| Josep Garnica | author | JGarnica22 | 0000-0001-9493-1321 | +| Scott Gigante | contributor | scottgigante | 0000-0002-4544-2764 | +| Kai Waldrant | contributor | KaiWaldrant | 0009-0003-8555-1361 | +| Martin Kim | contributor | martinkim0 | | +| Sai Nirmayi Yasa | contributor | sainirmayi | 0009-0003-6319-9803 | +| Tianyu Liu | contributor | HelloWorldLTY | 0000-0002-9412-6573 | +| Calvin McCarter | contributor | calvinmccarter | 0000-0002-7257-1350 | +| Daniel Schaffer | contributor | schafferde | | +| Stephen Chung | contributor | stephen-chung-mh | | +| Wendao Liu | contributor | liuwd15 | | ## API diff --git a/_viash.yaml b/_viash.yaml index 762a9c641..577806640 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -76,10 +76,11 @@ authors: info: github: jkobject orcid: 0000-0002-2818-9728 - - name: Seohyon Kim + - name: Seo Hyon Kim roles: [author] - info: + info: github: seohyonkim + orcid: 0009-0007-3062-4681 - name: Josep Garnica roles: [author] info: From 8e7984eb131f24b6f69f4a1b506b9b66d60c2f7b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 10:55:32 +0200 Subject: [PATCH 4/7] Apply suggestion from @stephen-chung-mh --- _viash.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/_viash.yaml b/_viash.yaml index 577806640..2b4458ddc 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -123,6 +123,7 @@ authors: roles: [contributor] info: github: stephen-chung-mh + orcid: 0009-0009-5833-9721 - name: Wendao Liu roles: [contributor] info: From 4dc93d38bb7f9cde596dc28b5f7685214d0bae56 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 11:40:29 +0200 Subject: [PATCH 5/7] Add pr number to changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a64b2e73..4bcd30edf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,7 @@ * Un-pin the scPRINT version and update parameters (PR #51) * Update scPRINT to better handle large datasets, including a new default model (PR #54) -* Credit contributors missing from the authors list, and fix Martin Kim's orcid. +* Credit contributors missing from the authors list, and fix Martin Kim's orcid (PR #100). ## Bug fixes From 3666b21fe63f197f06b0bb8dbd3617977c48608b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Aug 2026 11:44:42 +0200 Subject: [PATCH 6/7] rerender readme --- README.md | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 3ea4fca0e..82425f650 100644 --- a/README.md +++ b/README.md @@ -46,25 +46,25 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| Name | Roles | Github | Orcid | -|:------------------|:-------------------|:-----------------|:--------------------| -| Michaela Mueller | maintainer, author | mumichae | 0000-0002-1401-1785 | -| Malte Luecken | author | LuckyMD | 0000-0001-7464-7921 | -| Daniel Strobl | author | danielStrobl | 0000-0002-5516-7057 | -| Robrecht Cannoodt | author | rcannood | 0000-0003-3641-729X | -| Luke Zappia | author | lazappi | 0000-0001-7744-8565 | -| Jeremie Kalfon | author | jkobject | 0000-0002-2818-9728 | -| Seo Hyon Kim | author | seohyonkim | 0009-0007-3062-4681 | -| Josep Garnica | author | JGarnica22 | 0000-0001-9493-1321 | -| Scott Gigante | contributor | scottgigante | 0000-0002-4544-2764 | -| Kai Waldrant | contributor | KaiWaldrant | 0009-0003-8555-1361 | -| Martin Kim | contributor | martinkim0 | | -| Sai Nirmayi Yasa | contributor | sainirmayi | 0009-0003-6319-9803 | -| Tianyu Liu | contributor | HelloWorldLTY | 0000-0002-9412-6573 | -| Calvin McCarter | contributor | calvinmccarter | 0000-0002-7257-1350 | -| Daniel Schaffer | contributor | schafferde | | -| Stephen Chung | contributor | stephen-chung-mh | | -| Wendao Liu | contributor | liuwd15 | | +| Name | Roles | Orcid | Github | +|:------------------|:-------------------|:--------------------|:-----------------| +| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | +| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | +| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | +| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | +| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | +| Jeremie Kalfon | author | 0000-0002-2818-9728 | jkobject | +| Seo Hyon Kim | author | 0009-0007-3062-4681 | seohyonkim | +| Josep Garnica | author | 0000-0001-9493-1321 | JGarnica22 | +| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | +| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | +| Martin Kim | contributor | | martinkim0 | +| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | +| Tianyu Liu | contributor | 0000-0002-9412-6573 | HelloWorldLTY | +| Calvin McCarter | contributor | 0000-0002-7257-1350 | calvinmccarter | +| Daniel Schaffer | contributor | | schafferde | +| Stephen Chung | contributor | 0009-0009-5833-9721 | stephen-chung-mh | +| Wendao Liu | contributor | | liuwd15 | ## API From 4c457ca76dc0cab8baa99f0b9781ad42875f3670 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Aug 2026 06:07:59 +0200 Subject: [PATCH 7/7] add orcid, rerender readme --- README.md | 38 +++++++++++++++++++------------------- _viash.yaml | 1 + 2 files changed, 20 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 82425f650..a7899cbf1 100644 --- a/README.md +++ b/README.md @@ -46,25 +46,25 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| Name | Roles | Orcid | Github | -|:------------------|:-------------------|:--------------------|:-----------------| -| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | -| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | -| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | -| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | -| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | -| Jeremie Kalfon | author | 0000-0002-2818-9728 | jkobject | -| Seo Hyon Kim | author | 0009-0007-3062-4681 | seohyonkim | -| Josep Garnica | author | 0000-0001-9493-1321 | JGarnica22 | -| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | -| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | -| Martin Kim | contributor | | martinkim0 | -| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | -| Tianyu Liu | contributor | 0000-0002-9412-6573 | HelloWorldLTY | -| Calvin McCarter | contributor | 0000-0002-7257-1350 | calvinmccarter | -| Daniel Schaffer | contributor | | schafferde | -| Stephen Chung | contributor | 0009-0009-5833-9721 | stephen-chung-mh | -| Wendao Liu | contributor | | liuwd15 | +| Name | Roles | Github | Orcid | +|:------------------|:-------------------|:-----------------|:--------------------| +| Michaela Mueller | maintainer, author | mumichae | 0000-0002-1401-1785 | +| Malte Luecken | author | LuckyMD | 0000-0001-7464-7921 | +| Daniel Strobl | author | danielStrobl | 0000-0002-5516-7057 | +| Robrecht Cannoodt | author | rcannood | 0000-0003-3641-729X | +| Luke Zappia | author | lazappi | 0000-0001-7744-8565 | +| Jeremie Kalfon | author | jkobject | 0000-0002-2818-9728 | +| Seo Hyon Kim | author | seohyonkim | 0009-0007-3062-4681 | +| Josep Garnica | author | JGarnica22 | 0000-0001-9493-1321 | +| Scott Gigante | contributor | scottgigante | 0000-0002-4544-2764 | +| Kai Waldrant | contributor | KaiWaldrant | 0009-0003-8555-1361 | +| Martin Kim | contributor | martinkim0 | | +| Sai Nirmayi Yasa | contributor | sainirmayi | 0009-0003-6319-9803 | +| Tianyu Liu | contributor | HelloWorldLTY | 0000-0002-9412-6573 | +| Calvin McCarter | contributor | calvinmccarter | 0000-0002-7257-1350 | +| Daniel Schaffer | contributor | schafferde | | +| Stephen Chung | contributor | stephen-chung-mh | 0009-0009-5833-9721 | +| Wendao Liu | contributor | liuwd15 | 0000-0002-5124-9338 | ## API diff --git a/_viash.yaml b/_viash.yaml index 2b4458ddc..82732d580 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -128,6 +128,7 @@ authors: roles: [contributor] info: github: liuwd15 + orcid: 0000-0002-5124-9338 config_mods: | .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }