From 89a9d4bedc2302bdf7b713141d62aa2a2766c76e Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 7 Aug 2026 11:09:56 -0400 Subject: [PATCH 1/5] add faq entry --- docs/faq.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/docs/faq.rst b/docs/faq.rst index 78d2ace6..e0752a7a 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -153,6 +153,17 @@ For citing the actual code, we recommend looking at our Zenodo entry. You will find a variety of citation styles and ways to export it at |DOI|. +:ref:`(back to top) ` + +How is Dockstore's support for WDL 1.1? +------------------------ + +Support for WDL 1.1 is in-progress. Dockstore relies on an integration with Cromwell to parse WDL 1.1 and after `full support `__ was released in January 2026, we are working on adding full support to Dockstore. + +In the meantime, parsing of WDL imports in 1.1 remains functional, distribution of workflows via GA4GH TRS, and launching of workflows into platform partners such as `terra.bio `__ are functional. +Validation of WDL 1.1 workflows, the tools tab, and the DAG display will be non-functional. + + :ref:`(back to top) ` .. _faq-header-github-integration: From 889b1ec59f4c627c9b0dd6be0c4daf810f4d5803 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 7 Aug 2026 11:13:22 -0400 Subject: [PATCH 2/5] add note --- docs/faq.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/faq.rst b/docs/faq.rst index e0752a7a..7b2d72b4 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -163,6 +163,8 @@ Support for WDL 1.1 is in-progress. Dockstore relies on an integration with Crom In the meantime, parsing of WDL imports in 1.1 remains functional, distribution of workflows via GA4GH TRS, and launching of workflows into platform partners such as `terra.bio `__ are functional. Validation of WDL 1.1 workflows, the tools tab, and the DAG display will be non-functional. +Currently, a WDL workflow with only versions that are entirely WDL 1.1 cannot be published. A WDL workflow that has previous valid versions that are draft-2 or WDL 1.0 and has current versions that are WDL 1.1 can be published. +We are working to remove this restriction as a workaround. :ref:`(back to top) ` From 8100fe8a97d13b303b5017c2cf728fda938c92ea Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 7 Aug 2026 11:16:52 -0400 Subject: [PATCH 3/5] make build happier --- docs/faq.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/faq.rst b/docs/faq.rst index 7b2d72b4..36c542e4 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -156,7 +156,7 @@ You will find a variety of citation styles and ways to export it at :ref:`(back to top) ` How is Dockstore's support for WDL 1.1? ------------------------- +--------------------------------------- Support for WDL 1.1 is in-progress. Dockstore relies on an integration with Cromwell to parse WDL 1.1 and after `full support `__ was released in January 2026, we are working on adding full support to Dockstore. From fcea84c8605692b40fa57dc002f1aabc02ce88c2 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 7 Aug 2026 11:50:02 -0400 Subject: [PATCH 4/5] sigh at linkcheck --- docs/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/conf.py b/docs/conf.py index f6be4d16..9b002715 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -70,6 +70,7 @@ 'launch-with/galaxy-launch-with.html', 'launch-with/seqera-platform-launch-with.html', 'launch-with/terra-launch-with.html', 'launch-with/google-colab-launch-with.html', 'launch-with/github-codespaces-launch-with.html', 'launch-with/mybinder-launch-with.html', 'https://doi.org/*', + 'https://www.ucsc.edu/', # Confusing, linkcheck and curl report expired cert, but cert date is correct in browser 'https://support.orcid.org/hc/en-us/articles/360006971593-Do-you-have-more-than-one-account', # elwazi cert expired, remove when renewed From 9b35f9ed0f98cd2ea028c2f94fcbb5e0a73070c9 Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Fri, 7 Aug 2026 11:59:39 -0400 Subject: [PATCH 5/5] silly linkcheck --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 9b002715..9440b23d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -70,7 +70,7 @@ 'launch-with/galaxy-launch-with.html', 'launch-with/seqera-platform-launch-with.html', 'launch-with/terra-launch-with.html', 'launch-with/google-colab-launch-with.html', 'launch-with/github-codespaces-launch-with.html', 'launch-with/mybinder-launch-with.html', 'https://doi.org/*', - 'https://www.ucsc.edu/', + 'https://www.ucsc.edu', # Confusing, linkcheck and curl report expired cert, but cert date is correct in browser 'https://support.orcid.org/hc/en-us/articles/360006971593-Do-you-have-more-than-one-account', # elwazi cert expired, remove when renewed