From 6870beed46d5a09b96d6b082a5a30629554462e0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 15 Jan 2025 09:49:07 +0000 Subject: [PATCH 1/7] [automated] Update nf-core/tools API docs for dev --- .../api_reference/dev/api/pipelines/download.md | 2 +- .../docs/src/content/api_reference/dev/api/utils.md | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/download.md b/sites/docs/src/content/api_reference/dev/api/pipelines/download.md index 15e2978385..6833270667 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/download.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/download.md @@ -128,7 +128,7 @@ This is needed to symlink downloaded container images so Nextflow will find them #### `get_revision_hash(){:python}` -Find specified revision / branch hash +Find specified revision / branch / commit hash #### `get_singularity_images(current_revision: str = '') → None{:python}` diff --git a/sites/docs/src/content/api_reference/dev/api/utils.md b/sites/docs/src/content/api_reference/dev/api/utils.md index e1aca14b63..a74b4f1e0f 100644 --- a/sites/docs/src/content/api_reference/dev/api/utils.md +++ b/sites/docs/src/content/api_reference/dev/api/utils.md @@ -1637,6 +1637,18 @@ Returns the most recent container versions by default. ### `nf_core.utils.get_first_available_path(directory: Path | str, paths: List[str]) → Path | None{:python}` +### `nf_core.utils.get_repo_commit(pipeline, commit_id){:python}` + +Check if the repo contains the requested commit_id, and expand it to long form if necessary. + +- **Parameters:** + - **pipeline** (_str_) – GitHub repo username/repo + - **commit_id** – The requested commit ID (SHA). It can be in standard long/short form, or any length. +- **Returns:** + String or None +- **Return type:** + commit_id + ### `nf_core.utils.get_repo_releases_branches(pipeline, wfs){:python}` Fetches details of a nf-core workflow to download. From b7cea02cb9d2f4250918f3fbc647cc29b57888ed Mon Sep 17 00:00:00 2001 From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Date: Wed, 15 Jan 2025 11:39:23 +0100 Subject: [PATCH 2/7] Add yt link to bytesize_data_storage.md --- .../main-site/src/content/events/2025/bytesize_data_storage.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sites/main-site/src/content/events/2025/bytesize_data_storage.md b/sites/main-site/src/content/events/2025/bytesize_data_storage.md index c364734b17..e3f902e287 100644 --- a/sites/main-site/src/content/events/2025/bytesize_data_storage.md +++ b/sites/main-site/src/content/events/2025/bytesize_data_storage.md @@ -6,10 +6,11 @@ startDate: '2025-01-14' startTime: '13:00+01:00' endDate: '2025-01-14' endTime: '13:30+01:00' +youtubeEmbed: https://youtu.be/7wmaWU6-pYM locations: - name: Online links: - - https://kth-se.zoom.us/j/68390542812 + - https://youtu.be/7wmaWU6-pYM --- In this week's bytesize, Rob Syme ([@robsyme](https://github.com/robsyme)) introduces how the concepts that make Git so helpful might also be used to improve provenance tracking and collaboration when working with Nextflow workflows. Data and metadata are handled elegantly inside of Nextflow workflows, but sensibly handling metadata on the filesystem can be a challenge. Is there a way we can move away from using paths like `/data/do-not-delete/RELECOV/samples/SAMD00818643/NextSeq 550/202116335/paired/214115_S151_R1_001.fastq.gz.1`? From aff02af686e4fff883ec92a56e3cfbdf6989d738 Mon Sep 17 00:00:00 2001 From: Mateus Falco <162060565+mlfalco-bioinfo@users.noreply.github.com> Date: Wed, 15 Jan 2025 10:54:29 -0300 Subject: [PATCH 3/7] Create federal-technological-university-pr --- .../federal-technological-university-pr | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr diff --git a/sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr b/sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr new file mode 100644 index 0000000000..921af6f2ad --- /dev/null +++ b/sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr @@ -0,0 +1,25 @@ +--- +title: 'Hackathon - March 2025 (Federal Technological University of Paraná - UTFPR)' +subtitle: 'Local node of the nf-core hackathon at Federal Technological University of Paraná - UTFPR, Brazil' +shortTitle: '🇧🇷 Federal Technological University of Paraná - UTFPR' +type: 'hackathon' +startDate: '2025-03-24' +startTime: '09:00-03:00' +endDate: '2025-03-26' +endTime: '17:00-03:00' +locations: + - name: Federal Technological University of Paraná - UTFPR + address: | + Av. Profa. Laura Pacheco Bastos, 800 - Industrial, Guarapuava - PR, 85053-525 + links: + - https://maps.app.goo.gl/eGvbpGk1C2KBFJwB8 + geoCoordinates: [-25.3505666421501, -51.4795110688926] + +layout: '@layouts/events/HackathonMarch2025.astro' +--- + +Attendees from outside Federal Technological University of Paraná - UTFPR **can** attend. + +Main contact: Mateus Lucas Falco ([matlucfalco@gmail.com](mailto:matlucfalco@gmail.com)) + +Venue not yet booked, please check back later for more information. From 57ba087736e53b9a1d43d207b0fe11aeb5bb0733 Mon Sep 17 00:00:00 2001 From: matrulda Date: Wed, 15 Jan 2025 14:17:54 +0100 Subject: [PATCH 4/7] Update information about Uppsala local site for hackathon March 2025 --- .../uppsala-university.mdx | 20 ++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx b/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx index a78647375f..a18b62dc73 100644 --- a/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx +++ b/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx @@ -17,8 +17,22 @@ locations: layout: '@layouts/events/HackathonMarch2025.astro' --- -Attendees from outside Uppsala University **cannot** attend. +Attendees from outside Uppsala University **can** attend. -Main contact: Matilda Åslin ([matilda.aslin@medsci.uu.se](mailto:matilda.aslin@medsci.uu.se)) +Organizers: -Venue not yet booked, please check back later for more information. +- [ Matilda Åslin](https://nfcore.slack.com/team/UN7VCPD35) ([matilda.aslin@medsci.uu.se](mailto:matilda.aslin@medsci.uu.se)) +- [ Adrien Coulier](https://nfcore.slack.com/team/U044S8RL7K7) + +## Venue + +For anyone with access, this room is booked for the event: [E10:3303](https://link.mazemap.com/IrrlLmuc) + +## Access + +:::warning +If you do not already have access to Navet (main buidling of SciLifeLab Uppsala), you will not be able to access the room without assistance. Please be at entrace C11 before **9 am**, or, if that is not possible, inform one of the organizers on Slack at what time you will arrive, and they will pick you up. +::: + + +More info to come! Please check back later for more information. From 45bebe70cba0ce99a65895f28b1bad99adb354d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 16 Jan 2025 10:29:42 +0000 Subject: [PATCH 5/7] fix ref genomes link closes [404] Page not found: https://nf-co.re/docs/usage/offline #2934 --- sites/docs/src/content/docs/usage/Getting_started/offline.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sites/docs/src/content/docs/usage/Getting_started/offline.md b/sites/docs/src/content/docs/usage/Getting_started/offline.md index 14141ae34a..838d217540 100644 --- a/sites/docs/src/content/docs/usage/Getting_started/offline.md +++ b/sites/docs/src/content/docs/usage/Getting_started/offline.md @@ -58,7 +58,7 @@ For more information, see the [documentation for `nf-core pipelines download`](/ Some pipelines require reference genomes and have built-in integration with AWS-iGenomes. If you wish to use these references, you must download and transfer them to your offline cluster. -Once transferred, follow the [reference genomes documentation](/docs/usage/reference_genomes/reference_genomes.md) to configure the base path for the references. +Once transferred, follow the [reference genomes documentation](/docs/usage/reference_genomes) to configure the base path for the references. ## Bytesize talk From 6193848ce14f1c03b588ef65c14004bd251f9687 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 16 Jan 2025 11:33:16 +0100 Subject: [PATCH 6/7] Rename page, add to index.mdx table --- .../src/content/events/2025/hackathon-march-2025/index.mdx | 1 + .../{federal-technological-university-pr => utfpr_brazil.mdx} | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) rename sites/main-site/src/content/events/2025/hackathon-march-2025/{federal-technological-university-pr => utfpr_brazil.mdx} (86%) diff --git a/sites/main-site/src/content/events/2025/hackathon-march-2025/index.mdx b/sites/main-site/src/content/events/2025/hackathon-march-2025/index.mdx index 78b759dab3..b38d6eea2c 100644 --- a/sites/main-site/src/content/events/2025/hackathon-march-2025/index.mdx +++ b/sites/main-site/src/content/events/2025/hackathon-march-2025/index.mdx @@ -65,6 +65,7 @@ Even if you are attending a local site you will still join everyone online in Ga | ----------------- | ---------- | ---------------------------------------------- | -------------------------------------------------------------------------------------------------- | | 🇧🇪 Belgium | Ghent | Ghent University | [Read more](/events/2025/hackathon-march-2025/ghent-university) | | 🇧🇷 Brazil | Natal | Federal University of Rio Grande do Norte | [Read more](/events/2025/hackathon-march-2025/university-of-rio-grande-do-norte) | +| 🇧🇷 Brazil | Guarapuava | Federal Technological University of Paraná | [Read more](/events/2025/hackathon-march-2025/utfpr_brazil) | | 🇨🇿 Czech Republic | Brno | CEITEC MU | [Read more](/events/2025/hackathon-march-2025/ceitec-mu) | | 🇨🇴 Colombia | Bogota | University of the Andes | [Read more](/events/2025/hackathon-march-2025/bogota-colombia) | | 🇫🇷 France | Rennes | Institut of Genetics & Development of Rennes | [Read more](/events/2025/hackathon-march-2025/institut-of-genetics-development-of-rennes) | diff --git a/sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr b/sites/main-site/src/content/events/2025/hackathon-march-2025/utfpr_brazil.mdx similarity index 86% rename from sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr rename to sites/main-site/src/content/events/2025/hackathon-march-2025/utfpr_brazil.mdx index 921af6f2ad..6942e14509 100644 --- a/sites/main-site/src/content/events/2025/hackathon-march-2025/federal-technological-university-pr +++ b/sites/main-site/src/content/events/2025/hackathon-march-2025/utfpr_brazil.mdx @@ -10,8 +10,9 @@ endTime: '17:00-03:00' locations: - name: Federal Technological University of Paraná - UTFPR address: | - Av. Profa. Laura Pacheco Bastos, 800 - Industrial, Guarapuava - PR, 85053-525 + Av. Profa. Laura Pacheco Bastos, 800 - Industrial, Guarapuava - PR, 85053-525 links: + - https://www.utfpr.edu.br/campus/guarapuava - https://maps.app.goo.gl/eGvbpGk1C2KBFJwB8 geoCoordinates: [-25.3505666421501, -51.4795110688926] From 03566de93f12ed6f055ad7b601a7beee72f1e2e0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 16 Jan 2025 10:41:41 +0000 Subject: [PATCH 7/7] [automated] Fix code linting --- .../events/2025/hackathon-march-2025/uppsala-university.mdx | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx b/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx index a18b62dc73..c2be6692e2 100644 --- a/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx +++ b/sites/main-site/src/content/events/2025/hackathon-march-2025/uppsala-university.mdx @@ -21,8 +21,8 @@ Attendees from outside Uppsala University **can** attend. Organizers: -- [ Matilda Åslin](https://nfcore.slack.com/team/UN7VCPD35) ([matilda.aslin@medsci.uu.se](mailto:matilda.aslin@medsci.uu.se)) -- [ Adrien Coulier](https://nfcore.slack.com/team/U044S8RL7K7) +- [ Matilda Åslin](https://nfcore.slack.com/team/UN7VCPD35) ([matilda.aslin@medsci.uu.se](mailto:matilda.aslin@medsci.uu.se)) +- [ Adrien Coulier](https://nfcore.slack.com/team/U044S8RL7K7) ## Venue @@ -34,5 +34,4 @@ For anyone with access, this room is booked for the event: [E10:3303](https://li If you do not already have access to Navet (main buidling of SciLifeLab Uppsala), you will not be able to access the room without assistance. Please be at entrace C11 before **9 am**, or, if that is not possible, inform one of the organizers on Slack at what time you will arrive, and they will pick you up. ::: - More info to come! Please check back later for more information.