From 447220844601ec0928c224840e629c8803fb43f7 Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Mon, 27 Apr 2026 18:45:54 -0400 Subject: [PATCH 1/8] Fix stale .md cross-references to renamed side quests MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit PR #761 restructured side quests so `.md` became `/index.md` (URLs now `/side_quests//`), but missed updating cross-references that still point at the old `.md` filenames. Those links 404 on the deployed site — e.g., the "Debugging Nextflow Workflows" link from working_with_files. Replaces every stale `.md` link target with `/` across the English docs. Two segment names also rename: `nf-test.md` → `nf_test/` (the directory uses an underscore, not a hyphen). Translations are AI-regenerated each release, so they're not touched here. Affected English pages: side_quests/working_with_files/index.md side_quests/dev_environment/index.md nf4_science/genomics/02_per_sample_variant_calling.md hello_nextflow/02_hello_channels.md hello_nextflow/06_hello_config.md nextflow_run/next_steps.md nextflow_run/03_config.md hello_nf-core/02_rewrite_hello.md hello_nf-core/04_make_module.md Verified end-to-end against a local mkdocs build: every previously broken target now returns 200 (debugging, nf_test, metadata, workflows_of_workflows, working_with_files), and the user's specific link from working_with_files now resolves to /side_quests/debugging/. Co-Authored-By: Claude Opus 4.7 (1M context) Signed-off-by: Rob Syme --- docs/en/docs/hello_nextflow/02_hello_channels.md | 2 +- docs/en/docs/hello_nextflow/06_hello_config.md | 2 +- docs/en/docs/hello_nf-core/02_rewrite_hello.md | 6 +++--- docs/en/docs/hello_nf-core/04_make_module.md | 2 +- docs/en/docs/nextflow_run/03_config.md | 2 +- docs/en/docs/nextflow_run/next_steps.md | 2 +- .../nf4_science/genomics/02_per_sample_variant_calling.md | 2 +- docs/en/docs/side_quests/dev_environment/index.md | 2 +- docs/en/docs/side_quests/working_with_files/index.md | 2 +- 9 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/en/docs/hello_nextflow/02_hello_channels.md b/docs/en/docs/hello_nextflow/02_hello_channels.md index ac81a20f9e..2f04b88397 100644 --- a/docs/en/docs/hello_nextflow/02_hello_channels.md +++ b/docs/en/docs/hello_nextflow/02_hello_channels.md @@ -626,7 +626,7 @@ Success! Now we can add as many greetings as we like without worrying about outp In practice, naming files based on the input data itself is almost always impractical. The better way to generate dynamic filenames is to pass metadata to a process along with the input files. The metadata is typically provided via a 'sample sheet' or equivalents. - You'll learn how to do that later in your Nextflow training (see [Metadata side quest](../side_quests/metadata.md)). + You'll learn how to do that later in your Nextflow training (see [Metadata side quest](../side_quests/metadata/)). ### Takeaway diff --git a/docs/en/docs/hello_nextflow/06_hello_config.md b/docs/en/docs/hello_nextflow/06_hello_config.md index 91b88fb925..f532a764a9 100644 --- a/docs/en/docs/hello_nextflow/06_hello_config.md +++ b/docs/en/docs/hello_nextflow/06_hello_config.md @@ -1616,7 +1616,7 @@ This means that as long as we distribute any test data files with the workflow c We can point to URLs for larger files that are stored externally. Nextflow will download them automatically as long as there is an open connection. - For more details, see the Side Quest [Working with Files](../side_quests/working_with_files.md) + For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/) ### 6.3. Use `nextflow config` to see the resolved configuration diff --git a/docs/en/docs/hello_nf-core/02_rewrite_hello.md b/docs/en/docs/hello_nf-core/02_rewrite_hello.md index 8b8565d6c8..9166a1655b 100644 --- a/docs/en/docs/hello_nf-core/02_rewrite_hello.md +++ b/docs/en/docs/hello_nf-core/02_rewrite_hello.md @@ -8,13 +8,13 @@ If you're not familiar with the Hello pipeline or you could use a reminder, see !!! tip - This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/workflows_of_workflows.md) and [workflows of workflows](../side_quests/metadata.md), which are both covered in detail in the linked Side Quests. + This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/workflows_of_workflows/) and [workflows of workflows](../side_quests/metadata/), which are both covered in detail in the linked Side Quests. The instructions below includes the essential information you need in order to understand how these are used in the nf-core context, but it can be a lot to take in at once. If you have the time, we recommend working through the two Side Quests first (in no particular order): - - [Workflows of Workflows](../side_quests/workflows_of_workflows.md) - - [Metadata and meta maps](../side_quests/metadata.md) + - [Workflows of Workflows](../side_quests/workflows_of_workflows/) + - [Metadata and meta maps](../side_quests/metadata/) !!! note diff --git a/docs/en/docs/hello_nf-core/04_make_module.md b/docs/en/docs/hello_nf-core/04_make_module.md index 5d4c159f3e..86edde3a71 100644 --- a/docs/en/docs/hello_nf-core/04_make_module.md +++ b/docs/en/docs/hello_nf-core/04_make_module.md @@ -1273,7 +1273,7 @@ Each file serves a specific purpose: !!! tip "Learn more about testing" - The generated test file uses nf-test, a testing framework for Nextflow pipelines and modules. To learn how to write and run these tests, see the [nf-test side quest](../side_quests/nf-test.md). + The generated test file uses nf-test, a testing framework for Nextflow pipelines and modules. To learn how to write and run these tests, see the [nf-test side quest](../side_quests/nf_test/). The generated `main.nf` includes all the patterns you just learned, plus some additional features: diff --git a/docs/en/docs/nextflow_run/03_config.md b/docs/en/docs/nextflow_run/03_config.md index 15c8028064..e6110a3dd5 100644 --- a/docs/en/docs/nextflow_run/03_config.md +++ b/docs/en/docs/nextflow_run/03_config.md @@ -1347,7 +1347,7 @@ This means that as long as we distribute any test data files with the workflow c We can point to URLs for larger files that are stored externally. Nextflow will download them automatically as long as there is an open connection. - For more details, see the Side Quest [Working with Files](../side_quests/working_with_files.md) + For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/) ### 6.3. Use `nextflow config` to see the resolved configuration diff --git a/docs/en/docs/nextflow_run/next_steps.md b/docs/en/docs/nextflow_run/next_steps.md index 9a50c18cef..8ed74dd9f6 100644 --- a/docs/en/docs/nextflow_run/next_steps.md +++ b/docs/en/docs/nextflow_run/next_steps.md @@ -49,7 +49,7 @@ Here are our top suggestions for what to do next: - Don't just run Nextflow, write it! Become a Nextflow developer with [Hello Nextflow](../hello_nextflow/index.md) - Apply Nextflow to a scientific analysis use case with [Nextflow for Science](../nf4_science/index.md) - Get started with nf-core with [Hello nf-core](../hello_nf-core/index.md) -- Learn troubleshooting techniques with the [Debugging Side Quest](../side_quests/debugging.md) +- Learn troubleshooting techniques with the [Debugging Side Quest](../side_quests/debugging/) Finally, we recommend you have a look at [**Seqera Platform**](https://seqera.io/), a cloud-based platform developed by the creators of Nextflow that makes it even easier to launch and manage your workflows, as well as manage your data and run analyses interactively in any environment. diff --git a/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md b/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md index 4e14787a49..87bdaff5a2 100644 --- a/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md +++ b/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md @@ -560,7 +560,7 @@ Add variables for the accessory file paths inside the workflow block: ``` The `file()` syntax tells Nextflow explicitly to handle these inputs as file paths. -You can learn more about this in the Side Quest [Working with files](../../side_quests/working_with_files.md). +You can learn more about this in the Side Quest [Working with files](../../side_quests/working_with_files/). ### 2.2. Write the variant calling process and call it in the workflow diff --git a/docs/en/docs/side_quests/dev_environment/index.md b/docs/en/docs/side_quests/dev_environment/index.md index 66f5ce3e1b..3c24cf4ec2 100644 --- a/docs/en/docs/side_quests/dev_environment/index.md +++ b/docs/en/docs/side_quests/dev_environment/index.md @@ -617,7 +617,7 @@ We don't expect you to remember everything, but now you know that these features Apply these IDE skills while working through other training modules, for example: -- **[nf-test](nf-test.md)**: Create comprehensive test suites for your workflows +- **[nf-test](../nf_test/)**: Create comprehensive test suites for your workflows - **[Hello nf-core](../../hello_nf-core/)**: Build production-quality pipelines with community standards The true power of these IDE features emerges as you work on larger, more complex projects. Start incorporating them into your workflow gradually—within a few sessions, they'll become second nature and transform how you approach Nextflow development. diff --git a/docs/en/docs/side_quests/working_with_files/index.md b/docs/en/docs/side_quests/working_with_files/index.md index 4b183bb2ab..aeddc9fcfc 100644 --- a/docs/en/docs/side_quests/working_with_files/index.md +++ b/docs/en/docs/side_quests/working_with_files/index.md @@ -342,7 +342,7 @@ As you can see, it's a fairly straightforward little script that unzips the file The `debug true` directive in the process definition causes Nextflow to print the output from your script (like the line count "40") directly in the execution log. Without this, you would only see the process execution status but not the actual output from your script. - For more information on debugging Nextflow processes, see the [Debugging Nextflow Workflows](debugging.md) side quest. + For more information on debugging Nextflow processes, see the [Debugging Nextflow Workflows](../debugging/) side quest. With the module imported and its code examined, we can call the process from the workflow. From 6f3847299490f5e1d9c89090de27a91cedfa1f6c Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 19:12:03 -0400 Subject: [PATCH 2/8] Fix links to metadata and wow SQ --- docs/en/docs/hello_nf-core/02_rewrite_hello.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/en/docs/hello_nf-core/02_rewrite_hello.md b/docs/en/docs/hello_nf-core/02_rewrite_hello.md index 8b8565d6c8..ea592f79a0 100644 --- a/docs/en/docs/hello_nf-core/02_rewrite_hello.md +++ b/docs/en/docs/hello_nf-core/02_rewrite_hello.md @@ -8,13 +8,13 @@ If you're not familiar with the Hello pipeline or you could use a reminder, see !!! tip - This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/workflows_of_workflows.md) and [workflows of workflows](../side_quests/metadata.md), which are both covered in detail in the linked Side Quests. + This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/metadata/index.md) and [workflows of workflows](../side_quests/workflows_of_workflows/index.md), which are both covered in detail in the linked Side Quests. The instructions below includes the essential information you need in order to understand how these are used in the nf-core context, but it can be a lot to take in at once. If you have the time, we recommend working through the two Side Quests first (in no particular order): - - [Workflows of Workflows](../side_quests/workflows_of_workflows.md) - - [Metadata and meta maps](../side_quests/metadata.md) + - [Workflows of Workflows](../side_quests/workflows_of_workflows/index.md) + - [Metadata and meta maps](../side_quests/metadata/index.md) !!! note From 8fa379a5a44f0ee3e543830d16387353b3b5d15d Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 19:23:22 -0400 Subject: [PATCH 3/8] Add index.md to the side quest links --- docs/en/docs/hello_nextflow/02_hello_channels.md | 2 +- docs/en/docs/hello_nextflow/06_hello_config.md | 2 +- docs/en/docs/hello_nf-core/02_rewrite_hello.md | 6 +++--- docs/en/docs/hello_nf-core/04_make_module.md | 2 +- docs/en/docs/nextflow_run/03_config.md | 2 +- docs/en/docs/nextflow_run/next_steps.md | 2 +- .../nf4_science/genomics/02_per_sample_variant_calling.md | 2 +- docs/en/docs/side_quests/dev_environment/index.md | 2 +- docs/en/docs/side_quests/working_with_files/index.md | 2 +- 9 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/en/docs/hello_nextflow/02_hello_channels.md b/docs/en/docs/hello_nextflow/02_hello_channels.md index 2f04b88397..ae46e392e2 100644 --- a/docs/en/docs/hello_nextflow/02_hello_channels.md +++ b/docs/en/docs/hello_nextflow/02_hello_channels.md @@ -626,7 +626,7 @@ Success! Now we can add as many greetings as we like without worrying about outp In practice, naming files based on the input data itself is almost always impractical. The better way to generate dynamic filenames is to pass metadata to a process along with the input files. The metadata is typically provided via a 'sample sheet' or equivalents. - You'll learn how to do that later in your Nextflow training (see [Metadata side quest](../side_quests/metadata/)). + You'll learn how to do that later in your Nextflow training (see [Metadata side quest](../side_quests/metadata/index.md)). ### Takeaway diff --git a/docs/en/docs/hello_nextflow/06_hello_config.md b/docs/en/docs/hello_nextflow/06_hello_config.md index f532a764a9..58e19cb5bd 100644 --- a/docs/en/docs/hello_nextflow/06_hello_config.md +++ b/docs/en/docs/hello_nextflow/06_hello_config.md @@ -1616,7 +1616,7 @@ This means that as long as we distribute any test data files with the workflow c We can point to URLs for larger files that are stored externally. Nextflow will download them automatically as long as there is an open connection. - For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/) + For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/index.md) ### 6.3. Use `nextflow config` to see the resolved configuration diff --git a/docs/en/docs/hello_nf-core/02_rewrite_hello.md b/docs/en/docs/hello_nf-core/02_rewrite_hello.md index 9166a1655b..c13aa741be 100644 --- a/docs/en/docs/hello_nf-core/02_rewrite_hello.md +++ b/docs/en/docs/hello_nf-core/02_rewrite_hello.md @@ -8,13 +8,13 @@ If you're not familiar with the Hello pipeline or you could use a reminder, see !!! tip - This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/workflows_of_workflows/) and [workflows of workflows](../side_quests/metadata/), which are both covered in detail in the linked Side Quests. + This part of the course will introduce two important Nextflow mechanisms that are not covered in the Hello Nextflow introductory course: [meta maps](../side_quests/workflows_of_workflows/index.md) and [workflows of workflows](../side_quests/metadata/index.md), which are both covered in detail in the linked Side Quests. The instructions below includes the essential information you need in order to understand how these are used in the nf-core context, but it can be a lot to take in at once. If you have the time, we recommend working through the two Side Quests first (in no particular order): - - [Workflows of Workflows](../side_quests/workflows_of_workflows/) - - [Metadata and meta maps](../side_quests/metadata/) + - [Workflows of Workflows](../side_quests/workflows_of_workflows/index.md) + - [Metadata and meta maps](../side_quests/metadata/index.md) !!! note diff --git a/docs/en/docs/hello_nf-core/04_make_module.md b/docs/en/docs/hello_nf-core/04_make_module.md index 86edde3a71..6f80d916e9 100644 --- a/docs/en/docs/hello_nf-core/04_make_module.md +++ b/docs/en/docs/hello_nf-core/04_make_module.md @@ -1273,7 +1273,7 @@ Each file serves a specific purpose: !!! tip "Learn more about testing" - The generated test file uses nf-test, a testing framework for Nextflow pipelines and modules. To learn how to write and run these tests, see the [nf-test side quest](../side_quests/nf_test/). + The generated test file uses nf-test, a testing framework for Nextflow pipelines and modules. To learn how to write and run these tests, see the [nf-test side quest](../side_quests/nf_test/index.md). The generated `main.nf` includes all the patterns you just learned, plus some additional features: diff --git a/docs/en/docs/nextflow_run/03_config.md b/docs/en/docs/nextflow_run/03_config.md index e6110a3dd5..d1f4126169 100644 --- a/docs/en/docs/nextflow_run/03_config.md +++ b/docs/en/docs/nextflow_run/03_config.md @@ -1347,7 +1347,7 @@ This means that as long as we distribute any test data files with the workflow c We can point to URLs for larger files that are stored externally. Nextflow will download them automatically as long as there is an open connection. - For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/) + For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/index.md) ### 6.3. Use `nextflow config` to see the resolved configuration diff --git a/docs/en/docs/nextflow_run/next_steps.md b/docs/en/docs/nextflow_run/next_steps.md index 8ed74dd9f6..d9d8a64c28 100644 --- a/docs/en/docs/nextflow_run/next_steps.md +++ b/docs/en/docs/nextflow_run/next_steps.md @@ -49,7 +49,7 @@ Here are our top suggestions for what to do next: - Don't just run Nextflow, write it! Become a Nextflow developer with [Hello Nextflow](../hello_nextflow/index.md) - Apply Nextflow to a scientific analysis use case with [Nextflow for Science](../nf4_science/index.md) - Get started with nf-core with [Hello nf-core](../hello_nf-core/index.md) -- Learn troubleshooting techniques with the [Debugging Side Quest](../side_quests/debugging/) +- Learn troubleshooting techniques with the [Debugging Side Quest](../side_quests/debugging/index.md) Finally, we recommend you have a look at [**Seqera Platform**](https://seqera.io/), a cloud-based platform developed by the creators of Nextflow that makes it even easier to launch and manage your workflows, as well as manage your data and run analyses interactively in any environment. diff --git a/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md b/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md index 87bdaff5a2..8bc7f927e2 100644 --- a/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md +++ b/docs/en/docs/nf4_science/genomics/02_per_sample_variant_calling.md @@ -560,7 +560,7 @@ Add variables for the accessory file paths inside the workflow block: ``` The `file()` syntax tells Nextflow explicitly to handle these inputs as file paths. -You can learn more about this in the Side Quest [Working with files](../../side_quests/working_with_files/). +You can learn more about this in the Side Quest [Working with files](../../side_quests/working_with_files/index.md). ### 2.2. Write the variant calling process and call it in the workflow diff --git a/docs/en/docs/side_quests/dev_environment/index.md b/docs/en/docs/side_quests/dev_environment/index.md index 3c24cf4ec2..569e382d0c 100644 --- a/docs/en/docs/side_quests/dev_environment/index.md +++ b/docs/en/docs/side_quests/dev_environment/index.md @@ -617,7 +617,7 @@ We don't expect you to remember everything, but now you know that these features Apply these IDE skills while working through other training modules, for example: -- **[nf-test](../nf_test/)**: Create comprehensive test suites for your workflows +- **[nf-test](../nf_test/index.md)**: Create comprehensive test suites for your workflows - **[Hello nf-core](../../hello_nf-core/)**: Build production-quality pipelines with community standards The true power of these IDE features emerges as you work on larger, more complex projects. Start incorporating them into your workflow gradually—within a few sessions, they'll become second nature and transform how you approach Nextflow development. diff --git a/docs/en/docs/side_quests/working_with_files/index.md b/docs/en/docs/side_quests/working_with_files/index.md index aeddc9fcfc..afc6d5cc2c 100644 --- a/docs/en/docs/side_quests/working_with_files/index.md +++ b/docs/en/docs/side_quests/working_with_files/index.md @@ -342,7 +342,7 @@ As you can see, it's a fairly straightforward little script that unzips the file The `debug true` directive in the process definition causes Nextflow to print the output from your script (like the line count "40") directly in the execution log. Without this, you would only see the process execution status but not the actual output from your script. - For more information on debugging Nextflow processes, see the [Debugging Nextflow Workflows](../debugging/) side quest. + For more information on debugging Nextflow processes, see the [Debugging Nextflow Workflows](../debugging/index.md) side quest. With the module imported and its code examined, we can call the process from the workflow. From bb59caaa1e8e72cfce7b90ee758902944b37a74a Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 19:35:06 -0400 Subject: [PATCH 4/8] One more link fix --- docs/en/docs/side_quests/dev_environment/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/en/docs/side_quests/dev_environment/index.md b/docs/en/docs/side_quests/dev_environment/index.md index 1fa130016a..1a0451d419 100644 --- a/docs/en/docs/side_quests/dev_environment/index.md +++ b/docs/en/docs/side_quests/dev_environment/index.md @@ -618,7 +618,7 @@ We don't expect you to remember everything, but now you know that these features Apply these IDE skills while working through other training modules, for example: - **[nf-test](../nf_test/index.md)**: Create comprehensive test suites for your workflows -- **[Hello nf-core](../../hello_nf-core/)**: Build production-quality pipelines with community standards +- **[Hello nf-core](../../hello_nf-core/index.md)**: Build production-quality pipelines with community standards The true power of these IDE features emerges as you work on larger, more complex projects. Start incorporating them into your workflow gradually—within a few sessions, they'll become second nature and transform how you approach Nextflow development. From 5a24fb031c67034e7926ba629f2809982ffddc5c Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 19:55:14 -0400 Subject: [PATCH 5/8] Make all internal links point to the file --- .../docs/hello_nextflow/03_hello_workflow.md | 2 +- docs/en/docs/nf4_science/_template/index.md | 4 ++-- docs/en/docs/nf4_science/genomics/index.md | 4 ++-- docs/en/docs/nf4_science/imaging/index.md | 2 +- .../en/docs/nf4_science/imaging/next_steps.md | 4 ++-- docs/en/docs/nf4_science/index.md | 2 +- docs/en/docs/nf4_science/rnaseq/index.md | 4 ++-- docs/en/docs/side_quests/debugging/index.md | 10 ++++----- .../docs/side_quests/dev_environment/index.md | 4 ++-- .../essential_scripting_patterns/index.md | 2 +- docs/en/docs/side_quests/index.md | 22 +++++++++---------- docs/en/docs/side_quests/metadata/index.md | 2 +- .../splitting_and_grouping/index.md | 8 +++---- .../side_quests/working_with_files/index.md | 6 ++--- .../architects_toolkit_1.md | 2 +- docs/en/docs/training_collections/index.md | 4 ++-- 16 files changed, 41 insertions(+), 41 deletions(-) diff --git a/docs/en/docs/hello_nextflow/03_hello_workflow.md b/docs/en/docs/hello_nextflow/03_hello_workflow.md index 4fbc1f93a3..b29589ddc3 100644 --- a/docs/en/docs/hello_nextflow/03_hello_workflow.md +++ b/docs/en/docs/hello_nextflow/03_hello_workflow.md @@ -498,7 +498,7 @@ In theory this should handle any arbitrary number of input files. Some command-line tools require providing an argument (like `-input`) for each input file. In that case, we would have to do a little bit of extra work to compose the command. - You can see an example of this in the [Nextflow for Genomics](../../nf4_science/genomics/) training course. + You can see an example of this in the [Nextflow for Genomics](../../nf4_science/genomics/index.md) training course. ### 2.3. Add the collection step to the workflow diff --git a/docs/en/docs/nf4_science/_template/index.md b/docs/en/docs/nf4_science/_template/index.md index 39e1009816..e2bbcd02ad 100644 --- a/docs/en/docs/nf4_science/_template/index.md +++ b/docs/en/docs/nf4_science/_template/index.md @@ -14,14 +14,14 @@ additional_information: audience_prerequisites: - "**Audience:** This course is designed for researchers in {DOMAIN} and related fields who want to develop or customize data analysis pipelines." - "**Skills:** Some familiarity with the command line, basic scripting concepts, and common {DOMAIN} file formats is assumed." - - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/)." + - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/index.md)." --- # Nextflow for {DOMAIN} **A hands-on course applying Nextflow to a real-world {DOMAIN} use case: {METHOD_SHORT_DESCRIPTION}.** -This course builds on the [Hello Nextflow](../../hello_nextflow/) beginner training and demonstrates how to use Nextflow in the specific context of the {DOMAIN} domain. +This course builds on the [Hello Nextflow](../../hello_nextflow/index.md) beginner training and demonstrates how to use Nextflow in the specific context of the {DOMAIN} domain. You will implement a {METHOD} pipeline with [{TOOL_A}]({TOOL_A_URL}) and [{TOOL_B}]({TOOL_B_URL}). diff --git a/docs/en/docs/nf4_science/genomics/index.md b/docs/en/docs/nf4_science/genomics/index.md index 30ad1d9a7f..65811abb4d 100644 --- a/docs/en/docs/nf4_science/genomics/index.md +++ b/docs/en/docs/nf4_science/genomics/index.md @@ -14,14 +14,14 @@ additional_information: audience_prerequisites: - "**Audience:** This course is designed for researchers in genomics and related fields who want to develop or customize data analysis pipelines." - "**Skills:** Some familiarity with the command line, basic scripting concepts, and common genomics file formats is assumed." - - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/)." + - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/index.md)." --- # Nextflow for Genomics **A hands-on course applying Nextflow to a real-world genomics use case: variant calling with GATK.** -This course builds on the [Hello Nextflow](../../hello_nextflow/) beginner training and demonstrates how to use Nextflow in the specific context of the genomics domain. +This course builds on the [Hello Nextflow](../../hello_nextflow/index.md) beginner training and demonstrates how to use Nextflow in the specific context of the genomics domain. You will implement a variant calling pipeline with [GATK](https://gatk.broadinstitute.org/) (Genome Analysis Toolkit), a widely used software package for analyzing high-throughput sequencing data. diff --git a/docs/en/docs/nf4_science/imaging/index.md b/docs/en/docs/nf4_science/imaging/index.md index 3c146defa3..2fc949f016 100644 --- a/docs/en/docs/nf4_science/imaging/index.md +++ b/docs/en/docs/nf4_science/imaging/index.md @@ -33,4 +33,4 @@ This course assumes some minimal familiarity with the following: - Experience with the command line - Basic familiarity with imaging file formats (TIFF images, tabular data) -For technical requirements and environment setup, see the [Environment Setup](../../envsetup/) mini-course. +For technical requirements and environment setup, see the [Environment Setup](../../envsetup/index.md) mini-course. diff --git a/docs/en/docs/nf4_science/imaging/next_steps.md b/docs/en/docs/nf4_science/imaging/next_steps.md index 6f53a95e7a..c47ea5c471 100644 --- a/docs/en/docs/nf4_science/imaging/next_steps.md +++ b/docs/en/docs/nf4_science/imaging/next_steps.md @@ -16,8 +16,8 @@ Here are some recommended next steps to deepen your Nextflow knowledge: If you want to learn how to write Nextflow pipelines: -- **[Hello Nextflow](../../hello_nextflow/)**: Comprehensive Nextflow development training -- **[Side Quests](../../side_quests/)**: Advanced topics for pipeline developers +- **[Hello Nextflow](../../hello_nextflow/index.md)**: Comprehensive Nextflow development training +- **[Side Quests](../../side_quests/index.md)**: Advanced topics for pipeline developers ### Join the community diff --git a/docs/en/docs/nf4_science/index.md b/docs/en/docs/nf4_science/index.md index 1b9eaf0dd3..606e72e3ec 100644 --- a/docs/en/docs/nf4_science/index.md +++ b/docs/en/docs/nf4_science/index.md @@ -6,7 +6,7 @@ hide: # Nextflow for Science -These are courses that demonstrate how to apply the concepts and components presented in the [Hello Nextflow](../hello_nextflow/) beginner course to specific scientific use cases. Each course consists of a series of training modules that are designed to help learners build up their skills progressively. +These are courses that demonstrate how to apply the concepts and components presented in the [Hello Nextflow](../hello_nextflow/index.md) beginner course to specific scientific use cases. Each course consists of a series of training modules that are designed to help learners build up their skills progressively. !!! exercise "Nextflow for Genomics" diff --git a/docs/en/docs/nf4_science/rnaseq/index.md b/docs/en/docs/nf4_science/rnaseq/index.md index b7cbc89cbf..3f7f07a8db 100644 --- a/docs/en/docs/nf4_science/rnaseq/index.md +++ b/docs/en/docs/nf4_science/rnaseq/index.md @@ -15,14 +15,14 @@ additional_information: audience_prerequisites: - "**Audience:** This course is designed for researchers in transcriptomics and related fields who want to develop or customize data analysis pipelines." - "**Skills:** Some familiarity with the command line, basic scripting concepts, and common RNAseq file formats is assumed." - - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/)." + - "**Prerequisites:** Foundational Nextflow concepts and tooling covered in [Hello Nextflow](../../hello_nextflow/index.md)." --- # Nextflow for RNAseq **A hands-on course applying Nextflow to a real-world transcriptomics use case: bulk RNAseq processing with Trim Galore, HISAT2 and FastQC.** -This course builds on the [Hello Nextflow](../../hello_nextflow/) beginner training and demonstrates how to use Nextflow in the specific context of bulk RNAseq analysis. +This course builds on the [Hello Nextflow](../../hello_nextflow/index.md) beginner training and demonstrates how to use Nextflow in the specific context of bulk RNAseq analysis. You will implement a processing pipeline that trims adapter sequences, aligns reads to a genome reference and performs quality control (QC) at several stages. diff --git a/docs/en/docs/side_quests/debugging/index.md b/docs/en/docs/side_quests/debugging/index.md index c2d52e4dc6..d551dca364 100644 --- a/docs/en/docs/side_quests/debugging/index.md +++ b/docs/en/docs/side_quests/debugging/index.md @@ -18,10 +18,10 @@ By the end, you'll have a robust debugging methodology that transforms frustrati Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators) -**Optional:** We recommend completing the [IDE Features for Nextflow Development](../dev_environment/) side quest first. +**Optional:** We recommend completing the [IDE Features for Nextflow Development](../dev_environment/index.md) side quest first. That covers comprehensive coverage of IDE features that support debugging (syntax highlighting, error detection, etc.), which we'll use heavily here. --- @@ -598,7 +598,7 @@ process PROCESS_FILES { } ``` -In this example, we're defining the `prefix` variable in Bash, but in a Nexflow process the `$` syntax we used to refer to it (`#!groovy ${prefix}`) is interpreted as a Groovy variable, not Bash. The variable doesn't exist in the Groovy context, so we get a 'no such variable' error. +In this example, we're defining the `prefix` variable in Bash, but in a Nextflow process the `$` syntax we used to refer to it (`#!groovy ${prefix}`) is interpreted as a Groovy variable, not Bash. The variable doesn't exist in the Groovy context, so we get a 'no such variable' error. #### Fix the code @@ -1662,7 +1662,7 @@ nextflow run missing_software.nf -profile docker !!! note - To learn more about how Nextflow uses containers, see [Hello Nextflow](../hello_nextflow/05_hello_containers.md) + To learn more about how Nextflow uses containers, see [Hello Nextflow](../../hello_nextflow/05_hello_containers.md) ### 3.3. Bad resource configuration @@ -2192,7 +2192,7 @@ This methodology combines all the tools we've covered into an efficient workflow Once you've identified a problem, you need an efficient way to test your fixes without wasting time re-running successful parts of your workflow. Nextflow's `-resume` functionality is invaluable for debugging. - You will have encountered `-resume` if you've worked through [Hello Nextflow](../hello_nextflow/), and it's important that you make good use of it when debugging to save yourself waiting while the processes before your problem process run. + You will have encountered `-resume` if you've worked through [Hello Nextflow](../../hello_nextflow/index.md), and it's important that you make good use of it when debugging to save yourself waiting while the processes before your problem process run. **Resume debugging strategy:** diff --git a/docs/en/docs/side_quests/dev_environment/index.md b/docs/en/docs/side_quests/dev_environment/index.md index 1a0451d419..e84a1b9e22 100644 --- a/docs/en/docs/side_quests/dev_environment/index.md +++ b/docs/en/docs/side_quests/dev_environment/index.md @@ -8,7 +8,7 @@ Modern Integrated Development Environments (IDEs) can dramatically transform you ## What you should know first -This guide assumes you've completed the [Hello Nextflow](../hello_nextflow/) training course and are comfortable with foundational Nextflow concepts including: +This guide assumes you've completed the [Hello Nextflow](../hello_nextflow/index.md) training course and are comfortable with foundational Nextflow concepts including: - **Basic workflow structure**: Understanding processes, workflows, and how they connect together - **Channel operations**: Creating channels, passing data between processes, and using basic operators @@ -28,7 +28,7 @@ This guide focuses on **IDE productivity features** that will make you a more ef !!! info "Why IDE features now?" - You've likely already been using VS Code during the [Hello Nextflow](../hello_nextflow/) course, but we kept the focus on learning Nextflow fundamentals rather than IDE features. Now that you're comfortable with basic Nextflow concepts like processes, workflows, channels, and modules, you're ready to leverage the sophisticated IDE features that will make you a more efficient developer. + You've likely already been using VS Code during the [Hello Nextflow](../hello_nextflow/index.md) course, but we kept the focus on learning Nextflow fundamentals rather than IDE features. Now that you're comfortable with basic Nextflow concepts like processes, workflows, channels, and modules, you're ready to leverage the sophisticated IDE features that will make you a more efficient developer. Think of this as "leveling up" your development environment - the same editor you've been using has much more powerful capabilities that become truly valuable once you understand what they're helping you with. diff --git a/docs/en/docs/side_quests/essential_scripting_patterns/index.md b/docs/en/docs/side_quests/essential_scripting_patterns/index.md index 25dc2a64ee..90659100f3 100644 --- a/docs/en/docs/side_quests/essential_scripting_patterns/index.md +++ b/docs/en/docs/side_quests/essential_scripting_patterns/index.md @@ -442,7 +442,7 @@ This `[meta, file]` tuple structure is a common pattern in Nextflow for passing !!! note - **Maps and Metadata**: Maps are fundamental to working with metadata in Nextflow. For a more detailed explanation of working with metadata maps, see the [Working with metadata](../metadata/) side quest. + **Maps and Metadata**: Maps are fundamental to working with metadata in Nextflow. For a more detailed explanation of working with metadata maps, see the [Working with metadata](../metadata/index.md) side quest. Our workflow demonstrates the core pattern: **dataflow operations** (`workflow`, `channel.fromPath()`, `.splitCsv()`, `.map()`, `.view()`) orchestrate how data moves through the pipeline, while **scripting** (maps `[key: value]`, string methods, type conversions, ternary operators) inside the `.map()` closure handles the transformation of individual data items. diff --git a/docs/en/docs/side_quests/index.md b/docs/en/docs/side_quests/index.md index 01c2287144..37d109dc8e 100644 --- a/docs/en/docs/side_quests/index.md +++ b/docs/en/docs/side_quests/index.md @@ -36,17 +36,17 @@ If this is your first time exploring the Side Quests, start with the [Orientatio ### Side Quests -| Side Quest | Summary | Time Estimate | -| --------------------------------------------------------------- | ------------------------------------------------------------------------ | ------------- | -| [Development Environment](./dev_environment/) | Set up and configure a productive local Nextflow development environment | 45 mins | -| [Essential Scripting Patterns](./essential_scripting_patterns/) | Advanced scripting techniques for common workflow challenges | 90 mins | -| [File Input Processing](./working_with_files/) | File handling, path operations, and organizing outputs | 45 mins | -| [Metadata and Meta Maps](./metadata/) | Using metadata maps to track and propagate sample information | 45 mins | -| [Splitting and Grouping](./splitting_and_grouping/) | Techniques for splitting and regrouping data channels | 45 mins | -| [Testing with nf-test](./nf_test/) | Writing and running tests for Nextflow workflows | 1 hour | -| [Troubleshooting Workflows](./debugging/) | Identifying and fixing common workflow errors | 1 hour | -| [Workflows of Workflows](./workflows_of_workflows/) | Composing complex pipelines from reusable named workflow modules | 30 mins | -| [Plugin Development](./plugin_development/) | Using and building Nextflow plugins | 3 hours | +| Side Quest | Summary | Time Estimate | +| ----------------------------------------------------------------------- | ------------------------------------------------------------------------ | ------------- | +| [Development Environment](./dev_environment/index.md) | Set up and configure a productive local Nextflow development environment | 45 mins | +| [Essential Scripting Patterns](./essential_scripting_patterns/index.md) | Advanced scripting techniques for common workflow challenges | 90 mins | +| [File Input Processing](./working_with_files/index.md) | File handling, path operations, and organizing outputs | 45 mins | +| [Metadata and Meta Maps](./metadata/index.md) | Using metadata maps to track and propagate sample information | 45 mins | +| [Splitting and Grouping](./splitting_and_grouping/index.md) | Techniques for splitting and regrouping data channels | 45 mins | +| [Testing with nf-test](./nf_test/index.md) | Writing and running tests for Nextflow workflows | 1 hour | +| [Troubleshooting Workflows](./debugging/index.md) | Identifying and fixing common workflow errors | 1 hour | +| [Workflows of Workflows](./workflows_of_workflows/index.md) | Composing complex pipelines from reusable named workflow modules | 30 mins | +| [Plugin Development](./plugin_development/index.md) | Using and building Nextflow plugins | 3 hours | [Get started :material-arrow-right:](orientation.md){ .md-button .md-button--primary } diff --git a/docs/en/docs/side_quests/metadata/index.md b/docs/en/docs/side_quests/metadata/index.md index 83c5512ea0..cfb21716bf 100644 --- a/docs/en/docs/side_quests/metadata/index.md +++ b/docs/en/docs/side_quests/metadata/index.md @@ -1069,7 +1069,7 @@ Note that the output tuple is composed of `[meta, file, lang_id]`, meaning the m You must use keys instead. Meta maps provide an ideal structure for this purpose. - This use case is explored in detail in the [Splitting & Grouping](../splitting_and_grouping/) side quest. + This use case is explored in detail in the [Splitting & Grouping](../splitting_and_grouping/index.md) side quest. ### 2.2. Augment metadata with process outputs diff --git a/docs/en/docs/side_quests/splitting_and_grouping/index.md b/docs/en/docs/side_quests/splitting_and_grouping/index.md index 2fb702855e..b598e51a7f 100644 --- a/docs/en/docs/side_quests/splitting_and_grouping/index.md +++ b/docs/en/docs/side_quests/splitting_and_grouping/index.md @@ -29,7 +29,7 @@ Before taking on this side quest, you should: - Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators, working with files, meta data) -**Optional:** We recommend completing the [Metadata in workflows](../metadata/) side quest first. +**Optional:** We recommend completing the [Metadata in workflows](../metadata/index.md) side quest first. That covers the fundamentals of reading CSV files with `splitCsv` and creating meta maps, which we'll use heavily here. --- @@ -137,7 +137,7 @@ workflow { Throughout this tutorial, we'll use the `ch_` prefix for all channel variables to clearly indicate they are Nextflow channels. -If you completed the [Metadata in workflows](../metadata/) side quest, you'll recognize this pattern. We'll use `splitCsv` to read the CSV and immediately structure the data with a meta map to separate metadata from file paths. +If you completed the [Metadata in workflows](../metadata/index.md) side quest, you'll recognize this pattern. We'll use `splitCsv` to read the CSV and immediately structure the data with a meta map to separate metadata from file paths. !!! info @@ -662,7 +662,7 @@ To do so, first we define the closure as a new variable: We've defined the map transformation as a named variable that we can reuse. -Note that we also convert the file path to a Path object using `file()` so that any process receiving this channel can handle the file correctly (for more information see [Working with files](../working_with_files/)). +Note that we also convert the file path to a Path object using `file()` so that any process receiving this channel can handle the file correctly (for more information see [Working with files](../working_with_files/index.md)). Let's implement the closure in our workflow: @@ -1176,7 +1176,7 @@ Mastering these channel operations will enable you to build flexible, scalable p ### Key patterns -1. **Creating structured input data:** Starting from a CSV file with meta maps (building on patterns from [Metadata in workflows](../metadata/)) +1. **Creating structured input data:** Starting from a CSV file with meta maps (building on patterns from [Metadata in workflows](../metadata/index.md)) ```groovy ch_samples = channel.fromPath("./data/samplesheet.csv") diff --git a/docs/en/docs/side_quests/working_with_files/index.md b/docs/en/docs/side_quests/working_with_files/index.md index afc6d5cc2c..82f7aa4321 100644 --- a/docs/en/docs/side_quests/working_with_files/index.md +++ b/docs/en/docs/side_quests/working_with_files/index.md @@ -25,7 +25,7 @@ These skills will help you build workflows that can handle different kinds of fi Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../../hello_nextflow/) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators) @@ -1614,7 +1614,7 @@ process ANALYZE_READS { !!! note We are calling our metadata map `meta` by convention. - For a deeper dive into meta maps, see the [Metadata and meta maps](../metadata/) side quest. + For a deeper dive into meta maps, see the [Metadata and meta maps](../metadata/index.md) side quest. With the `ANALYZE_READS` process imported and its code reviewed, we can add a call to it in the workflow. @@ -1960,7 +1960,7 @@ There's a lot more you can do once you have your metadata loaded into a map like 3. Split, join, and recombine data based on metadata values This pattern of keeping metadata explicit and attached to the data (rather than encoded in filenames) is a core best practice in Nextflow that enables building robust, maintainable analysis workflows. -You can learn more about this in the [Metadata and meta maps](../metadata/) side quest. +You can learn more about this in the [Metadata and meta maps](../metadata/index.md) side quest. ### Takeaway diff --git a/docs/en/docs/training_collections/architects_toolkit_1.md b/docs/en/docs/training_collections/architects_toolkit_1.md index b836664ccf..4ff6f44599 100644 --- a/docs/en/docs/training_collections/architects_toolkit_1.md +++ b/docs/en/docs/training_collections/architects_toolkit_1.md @@ -25,7 +25,7 @@ This collection is designed for users who have completed the basic Nextflow trai **Prerequisites** -- Completion of [Hello Nextflow](../../hello_nextflow/) training or equivalent experience +- Completion of [Hello Nextflow](../../hello_nextflow/index.md) training or equivalent experience - Basic familiarity with Nextflow syntax and concepts - Understanding of basic workflow development patterns - Experience with command-line tools diff --git a/docs/en/docs/training_collections/index.md b/docs/en/docs/training_collections/index.md index abf63ee87d..2acedcab47 100644 --- a/docs/en/docs/training_collections/index.md +++ b/docs/en/docs/training_collections/index.md @@ -13,9 +13,9 @@ This section contains curated collections of training modules called [Side Quest Each collection has specific prerequisites documented on its index page. However, most collections assume: - Experience with the command line -- Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../../hello_nextflow/) beginner training course +- Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../../hello_nextflow/index.md) beginner training course -For technical requirements and environment setup, see the [Environment Setup](../../envsetup/) mini-course. +For technical requirements and environment setup, see the [Environment Setup](../../envsetup/index.md) mini-course. ## Available collections From 4fdcb0208c9950da03cf3fdcb34e2d4cafa8d48c Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 20:26:55 -0400 Subject: [PATCH 6/8] Fix remaining broken links --- docs/en/docs/hello_nextflow/03_hello_workflow.md | 2 +- docs/en/docs/hello_nf-core/03_use_module.md | 2 +- docs/en/docs/hello_nf-core/05_input_validation.md | 2 +- docs/en/docs/index.md | 10 +++++----- docs/en/docs/nf4_science/imaging/04_config.md | 6 +++--- docs/en/docs/nf4_science/index.md | 6 +++--- docs/en/docs/side_quests/debugging/index.md | 4 ++-- docs/en/docs/side_quests/dev_environment/index.md | 4 ++-- .../essential_scripting_patterns/index.md | 8 ++++---- docs/en/docs/side_quests/metadata/index.md | 12 ++++++------ docs/en/docs/side_quests/nf_test/index.md | 14 +++++++------- .../docs/side_quests/plugin_development/index.md | 2 +- .../side_quests/splitting_and_grouping/index.md | 6 +++--- .../side_quests/workflows_of_workflows/index.md | 6 +++--- .../docs/side_quests/working_with_files/index.md | 6 ++---- .../training_collections/architects_toolkit_1.md | 12 ++++++------ docs/en/docs/training_collections/index.md | 4 ++-- 17 files changed, 52 insertions(+), 54 deletions(-) diff --git a/docs/en/docs/hello_nextflow/03_hello_workflow.md b/docs/en/docs/hello_nextflow/03_hello_workflow.md index b29589ddc3..1d8a240910 100644 --- a/docs/en/docs/hello_nextflow/03_hello_workflow.md +++ b/docs/en/docs/hello_nextflow/03_hello_workflow.md @@ -498,7 +498,7 @@ In theory this should handle any arbitrary number of input files. Some command-line tools require providing an argument (like `-input`) for each input file. In that case, we would have to do a little bit of extra work to compose the command. - You can see an example of this in the [Nextflow for Genomics](../../nf4_science/genomics/index.md) training course. + You can see an example of this in the [Nextflow for Genomics](../nf4_science/genomics/index.md) training course. ### 2.3. Add the collection step to the workflow diff --git a/docs/en/docs/hello_nf-core/03_use_module.md b/docs/en/docs/hello_nf-core/03_use_module.md index 40bfd57773..b01c454ae7 100644 --- a/docs/en/docs/hello_nf-core/03_use_module.md +++ b/docs/en/docs/hello_nf-core/03_use_module.md @@ -512,7 +512,7 @@ Not only does it allow you to name outputs based on metadata, but you can also d !!! note "Learn more about metadata" - For a comprehensive introduction to working with metadata in Nextflow workflows, including how to read metadata from samplesheets and use it to customize processing, see the [Metadata in workflows](../side_quests/metadata) side quest. + For a comprehensive introduction to working with metadata in Nextflow workflows, including how to read metadata from samplesheets and use it to customize processing, see the [Metadata in workflows](../side_quests/metadata/index.md) side quest. ### 2.3. Summarize changes to be made diff --git a/docs/en/docs/hello_nf-core/05_input_validation.md b/docs/en/docs/hello_nf-core/05_input_validation.md index 015f89d9ee..b991fa2221 100644 --- a/docs/en/docs/hello_nf-core/05_input_validation.md +++ b/docs/en/docs/hello_nf-core/05_input_validation.md @@ -791,4 +791,4 @@ You've implemented and tested both parameter validation and input data validatio You've completed all five parts of the Hello nf-core training course! -Continue to the [Summary](summary.md) to reflect on what you've built and learned. +Continue to the [Summary](next_steps.md) to reflect on what you've built and learned. diff --git a/docs/en/docs/index.md b/docs/en/docs/index.md index 7f950ad916..7c27187fec 100644 --- a/docs/en/docs/index.md +++ b/docs/en/docs/index.md @@ -101,19 +101,19 @@ hide: For researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline. - [Start the Nextflow for Genomics training :material-arrow-right:](nf4_science/genomics/){ .md-button .md-button--secondary } + [Start the Nextflow for Genomics training :material-arrow-right:](nf4_science/genomics/index.md){ .md-button .md-button--secondary } ??? courses "**Nextflow for RNAseq** (bulk RNAseq)" For researchers who wish to learn how to develop their own RNAseq pipelines. The course uses a bulk RNAseq processing use case to demonstrate how to develop a simple but functional RNAseq pipeline. - [Start the Nextflow for RNAseq training :material-arrow-right:](nf4_science/rnaseq/){ .md-button .md-button--secondary } + [Start the Nextflow for RNAseq training :material-arrow-right:](nf4_science/rnaseq/index.md){ .md-button .md-button--secondary } ??? courses "**Nextflow for Imaging** (spatial omics)" For researchers in imaging and spatial omics who wish to learn how to run and customize analysis pipelines. The course uses the nf-core/molkart pipeline to provide a biologically-relevant pipeline demonstrate how to run, configure, and manage inputs for Nextflow pipelines workflows. - [Start the Nextflow for Imaging training :material-arrow-right:](nf4_science/imaging/){ .md-button .md-button--secondary } + [Start the Nextflow for Imaging training :material-arrow-right:](nf4_science/imaging/index.md){ .md-button .md-button--secondary } - :material-run:{ .lg .middle } __Advanced track__ @@ -142,13 +142,13 @@ hide: Standalone mini-courses intended for Nextflow developers who wish to widen their range and/or deepen their skills on particular topics. They are presented linearly but can be taken in any order (see dependencies in each mini-course overview). - [Browse the Side Quests :material-arrow-right:](side_quests/){ .md-button .md-button--secondary } + [Browse the Side Quests :material-arrow-right:](side_quests/index.md){ .md-button .md-button--secondary } ??? courses "**Training Collections:** Recommended learning paths through the Side Quests" Training Collections combine multiple Side Quests in order to provide a comprehensive learning experience around a particular theme or use case. - [Browse the Training Collections :material-arrow-right:](training_collections/){ .md-button .md-button--secondary } + [Browse the Training Collections :material-arrow-right:](training_collections/index.md){ .md-button .md-button--secondary } diff --git a/docs/en/docs/nf4_science/imaging/04_config.md b/docs/en/docs/nf4_science/imaging/04_config.md index 930c7d246d..f174340350 100644 --- a/docs/en/docs/nf4_science/imaging/04_config.md +++ b/docs/en/docs/nf4_science/imaging/04_config.md @@ -445,6 +445,6 @@ Congratulations on completing the Nextflow for Bioimaging course! Next steps: - Fill out the course survey to provide feedback -- Check out [Hello Nextflow](../hello_nextflow/index.md) to learn more about developing workflows -- Explore [Hello nf-core](../hello_nf-core/index.md) to dive deeper into nf-core tooling -- Browse other courses in the [training collections](../training_collections/index.md) +- Check out [Hello Nextflow](../../hello_nextflow/index.md) to learn more about developing workflows +- Explore [Hello nf-core](../../hello_nf-core/index.md) to dive deeper into nf-core tooling +- Browse other courses in the [training collections](../../training_collections/index.md) diff --git a/docs/en/docs/nf4_science/index.md b/docs/en/docs/nf4_science/index.md index 606e72e3ec..1b05f569d5 100644 --- a/docs/en/docs/nf4_science/index.md +++ b/docs/en/docs/nf4_science/index.md @@ -16,7 +16,7 @@ These are courses that demonstrate how to apply the concepts and components pres This is a course for researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline. - [Start the Nextflow for Genomics training :material-arrow-right:](genomics/){ .md-button .md-button--primary } + [Start the Nextflow for Genomics training :material-arrow-right:](genomics/index.md){ .md-button .md-button--primary } !!! exercise "Nextflow for RNAseq" @@ -26,7 +26,7 @@ These are courses that demonstrate how to apply the concepts and components pres This is a course for researchers who wish to learn how to develop their own RNAseq pipelines. The course uses a bulk RNAseq processing use case to demonstrate how to develop a simple but functional RNAseq pipeline. - [Start the Nextflow for RNAseq training :material-arrow-right:](rnaseq/){ .md-button .md-button--primary } + [Start the Nextflow for RNAseq training :material-arrow-right:](rnaseq/index.md){ .md-button .md-button--primary } !!! exercise "Nextflow for Bioimaging" @@ -36,6 +36,6 @@ These are courses that demonstrate how to apply the concepts and components pres This is a course for researchers who wish to learn how to run and configure bioimaging pipelines. The course uses nf-core/molkart to demonstrate essential Nextflow usage patterns applicable to any pipeline. - [Start the Nextflow for Bioimaging training :material-arrow-right:](imaging/){ .md-button .md-button--primary } + [Start the Nextflow for Bioimaging training :material-arrow-right:](imaging/index.md){ .md-button .md-button--primary } Let us know what other domains and use cases you'd like to see covered here by posting in the [Training section](https://community.seqera.io/c/training/) of the community forum. diff --git a/docs/en/docs/side_quests/debugging/index.md b/docs/en/docs/side_quests/debugging/index.md index d551dca364..6c23af0c25 100644 --- a/docs/en/docs/side_quests/debugging/index.md +++ b/docs/en/docs/side_quests/debugging/index.md @@ -30,7 +30,7 @@ That covers comprehensive coverage of IDE features that support debugging (synta #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -2656,4 +2656,4 @@ For production workflows, consider: ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/dev_environment/index.md b/docs/en/docs/side_quests/dev_environment/index.md index e84a1b9e22..9702f9124a 100644 --- a/docs/en/docs/side_quests/dev_environment/index.md +++ b/docs/en/docs/side_quests/dev_environment/index.md @@ -8,7 +8,7 @@ Modern Integrated Development Environments (IDEs) can dramatically transform you ## What you should know first -This guide assumes you've completed the [Hello Nextflow](../hello_nextflow/index.md) training course and are comfortable with foundational Nextflow concepts including: +This guide assumes you've completed the [Hello Nextflow](../../hello_nextflow/index.md) training course and are comfortable with foundational Nextflow concepts including: - **Basic workflow structure**: Understanding processes, workflows, and how they connect together - **Channel operations**: Creating channels, passing data between processes, and using basic operators @@ -28,7 +28,7 @@ This guide focuses on **IDE productivity features** that will make you a more ef !!! info "Why IDE features now?" - You've likely already been using VS Code during the [Hello Nextflow](../hello_nextflow/index.md) course, but we kept the focus on learning Nextflow fundamentals rather than IDE features. Now that you're comfortable with basic Nextflow concepts like processes, workflows, channels, and modules, you're ready to leverage the sophisticated IDE features that will make you a more efficient developer. + You've likely already been using VS Code during the [Hello Nextflow](../../hello_nextflow/index.md) course, but we kept the focus on learning Nextflow fundamentals rather than IDE features. Now that you're comfortable with basic Nextflow concepts like processes, workflows, channels, and modules, you're ready to leverage the sophisticated IDE features that will make you a more efficient developer. Think of this as "leveling up" your development environment - the same editor you've been using has much more powerful capabilities that become truly valuable once you understand what they're helping you with. diff --git a/docs/en/docs/side_quests/essential_scripting_patterns/index.md b/docs/en/docs/side_quests/essential_scripting_patterns/index.md index 90659100f3..95fdb87d11 100644 --- a/docs/en/docs/side_quests/essential_scripting_patterns/index.md +++ b/docs/en/docs/side_quests/essential_scripting_patterns/index.md @@ -24,7 +24,7 @@ We'll transform a simple CSV-reading workflow into a sophisticated bioinformatic Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators, working with files, meta data) - Have basic familiarity with common programming constructs (variables, maps, lists) @@ -37,7 +37,7 @@ We'll start with fundamental concepts and build up to advanced patterns. #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -977,7 +977,7 @@ fastp \ --thread 2 ``` -Another common usage of dynamic script logic can be seen in [the Nextflow for Science Genomics module](../../nf4science/genomics/02_joint_calling). In that module, the GATK process being called can take multiple input files, but each must be prefixed with `-V` to form a correct command line. The process uses scripting to transform a collection of input files (`all_gvcfs`) into the correct command arguments: +Another common usage of dynamic script logic can be seen in [the Nextflow for Science Genomics module](../../nf4_science/genomics/03_joint_calling.md). In that module, the GATK process being called can take multiple input files, but each must be prefixed with `-V` to form a correct command line. The process uses scripting to transform a collection of input files (`all_gvcfs`) into the correct command arguments: ```groovy title="command line manipulation for GATK" linenums="1" hl_lines="2 5" script: @@ -2456,4 +2456,4 @@ You'll benefit from practicing and expanding your skills in order to: ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/metadata/index.md b/docs/en/docs/side_quests/metadata/index.md index cfb21716bf..7c8bb794be 100644 --- a/docs/en/docs/side_quests/metadata/index.md +++ b/docs/en/docs/side_quests/metadata/index.md @@ -30,7 +30,7 @@ These skills will help you build more robust and flexible pipelines that can han Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators) --- @@ -39,7 +39,7 @@ Before taking on this side quest, you should: #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -193,7 +193,7 @@ output { The [`splitCsv`](https://www.nextflow.io/docs/latest/reference/operator.html#splitcsv) operator reads each row in the file as a channel element. This is the same approach we use to load CSV data in Hello Nextflow, our beginner course. -Have a look at [this section](../../hello_nextflow/02_hello_channels/#4-read-input-values-from-a-csv-file) if you need a reminder of how that works. +Have a look at [this section](../../hello_nextflow/02_hello_channels.md#4-read-input-values-from-a-csv-file) if you need a reminder of how that works. With `header: true`, the first row is treated as column headers, so each element becomes a map of key-value pairs keyed by column name. @@ -299,7 +299,7 @@ To access the `character` column, add the `map` operation before the `.view()` o .view() ``` -This way of accessing a specific field is explained in more detail in [this section](../../hello_nextflow/02_hello_channels/#43-use-the-map-operator-to-extract-the-greetings) of Hello Nextflow, if you need a reminder of how that works. +This way of accessing a specific field is explained in more detail in [this section](../../hello_nextflow/02_hello_channels.md#43-use-the-map-operator-to-extract-the-greetings) of Hello Nextflow, if you need a reminder of how that works. #### 1.2.2. Run the workflow @@ -1627,7 +1627,7 @@ There are two complementary approaches to make workflows more robust against mis **1. Input validation** The most reliable solution is to validate the datasheet before any processing begins, so problems are caught early with a clear error message rather than surfacing as a cryptic process failure mid-run. -The [Hello nf-core](../hello_nf-core/05_input_validation.md) training covers how to add input validation using the nf-schema plugin. +The [Hello nf-core](../../hello_nf-core/05_input_validation.md) training covers how to add input validation using the nf-schema plugin. **2. Explicit process inputs for required values** @@ -1731,4 +1731,4 @@ The "meta map + data file" tuple pattern is a core convention in Nextflow, offer ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/nf_test/index.md b/docs/en/docs/side_quests/nf_test/index.md index 8986176030..72ca64f083 100644 --- a/docs/en/docs/side_quests/nf_test/index.md +++ b/docs/en/docs/side_quests/nf_test/index.md @@ -45,7 +45,7 @@ These skills will help you implement a comprehensive testing strategy in your pi Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators, working with files, meta data) --- @@ -54,7 +54,7 @@ Before taking on this side quest, you should: #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -82,13 +82,13 @@ You'll find a main workflow file and a CSV file called `greetings.csv` that cont └── main.nf ``` -For a detailed description of the files, see the [warmup from Hello Nextflow](../hello_nextflow/00_orientation.md). +For a detailed description of the files, see the [warmup from Hello Nextflow](../../hello_nextflow/00_orientation.md). -The workflow we'll be testing is a subset of the Hello workflow built in [Hello Workflow](../hello_nextflow/03_hello_workflow.md). +The workflow we'll be testing is a subset of the Hello workflow built in [Hello Workflow](../../hello_nextflow/03_hello_workflow.md). ??? example "What does the Hello Nextflow workflow do?" - If you haven't done the [Hello Nextflow](../hello_nextflow/index.md) training, here's a quick overview of what this simple workflow does. + If you haven't done the [Hello Nextflow](../../hello_nextflow/index.md) training, here's a quick overview of what this simple workflow does. The workflow takes a CSV file containing greetings, runs four consecutive transformation steps on them, and outputs a single text file containing an ASCII picture of a fun character saying the greetings. @@ -733,7 +733,7 @@ Test Process sayHello FAILURE: Executed 1 tests in 4.884s (1 failed) ``` -The test fails because the `sayHello` process declares 1 input but was called with 0 arguments. Let's fix that by adding an input to the process. Remember from [Hello Workflow](../hello_nextflow/03_hello_workflow.md) (and the warmup section above) that our `sayHello` process takes a single value input, which we will need to provide. We should also fix the test name to better reflect what we're testing. +The test fails because the `sayHello` process declares 1 input but was called with 0 arguments. Let's fix that by adding an input to the process. Remember from [Hello Workflow](../../hello_nextflow/03_hello_workflow.md) (and the warmup section above) that our `sayHello` process takes a single value input, which we will need to provide. We should also fix the test name to better reflect what we're testing. === "After" @@ -1200,4 +1200,4 @@ Check out the [nf-test documentation](https://www.nf-test.com/) for more advance ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/plugin_development/index.md b/docs/en/docs/side_quests/plugin_development/index.md index 995659aff0..321ad560e8 100644 --- a/docs/en/docs/side_quests/plugin_development/index.md +++ b/docs/en/docs/side_quests/plugin_development/index.md @@ -19,7 +19,7 @@ No prior Java or Groovy experience is required. **Prerequisites** -- A GitHub account OR a local installation as described [here](../../envsetup/02_local). +- A GitHub account OR a local installation as described [here](../../envsetup/02_local.md). - Completed the [Hello Nextflow](../../hello_nextflow/index.md) course or equivalent. - Java 21 or later (included in the training environment; only needed for Parts 2-6). diff --git a/docs/en/docs/side_quests/splitting_and_grouping/index.md b/docs/en/docs/side_quests/splitting_and_grouping/index.md index b598e51a7f..8ba55a1cf9 100644 --- a/docs/en/docs/side_quests/splitting_and_grouping/index.md +++ b/docs/en/docs/side_quests/splitting_and_grouping/index.md @@ -26,7 +26,7 @@ These skills will help you build workflows that can handle multiple input files Before taking on this side quest, you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators, working with files, meta data) **Optional:** We recommend completing the [Metadata in workflows](../metadata/index.md) side quest first. @@ -38,7 +38,7 @@ That covers the fundamentals of reading CSV files with `splitCsv` and creating m #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -1257,4 +1257,4 @@ Mastering these channel operations will enable you to build flexible, scalable p ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/workflows_of_workflows/index.md b/docs/en/docs/side_quests/workflows_of_workflows/index.md index 2fc8755483..93df9997f5 100644 --- a/docs/en/docs/side_quests/workflows_of_workflows/index.md +++ b/docs/en/docs/side_quests/workflows_of_workflows/index.md @@ -22,7 +22,7 @@ These skills will help you build complex pipelines while maintaining clean, main Before taking on this side quest you should: -- Have completed the [Hello Nextflow](../hello_nextflow/README.md) tutorial or equivalent beginner's course. +- Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators, modules) --- @@ -31,7 +31,7 @@ Before taking on this side quest you should: #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -722,4 +722,4 @@ Applying these techniques in your own work will enable you to build more sophist ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/side_quests/working_with_files/index.md b/docs/en/docs/side_quests/working_with_files/index.md index 82f7aa4321..7dbe1ce8aa 100644 --- a/docs/en/docs/side_quests/working_with_files/index.md +++ b/docs/en/docs/side_quests/working_with_files/index.md @@ -28,15 +28,13 @@ Before taking on this side quest, you should: - Have completed the [Hello Nextflow](../../hello_nextflow/index.md) tutorial or equivalent beginner's course. - Be comfortable using basic Nextflow concepts and mechanisms (processes, channels, operators) - - --- ## 0. Get started #### Open the training codespace -If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../envsetup/index.md). +If you haven't yet done so, make sure to open the training environment as described in the [Environment Setup](../../envsetup/index.md). [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master) @@ -2113,4 +2111,4 @@ Applying these techniques in your own work will enable you to build more efficie ## What's next? -Return to the [menu of Side Quests](../) or click the button in the bottom right of the page to move on to the next topic in the list. +Return to the [menu of Side Quests](../index.md) or click the button in the bottom right of the page to move on to the next topic in the list. diff --git a/docs/en/docs/training_collections/architects_toolkit_1.md b/docs/en/docs/training_collections/architects_toolkit_1.md index 4ff6f44599..d32eb81793 100644 --- a/docs/en/docs/training_collections/architects_toolkit_1.md +++ b/docs/en/docs/training_collections/architects_toolkit_1.md @@ -6,7 +6,7 @@ hide: # The Architect's Toolkit I -Our Training Collections provide curated learning paths through our advanced training materials (called [Side Quests](../../side_quests)). This collection covers four essential topics that are frequently used together for building robust and scalable workflows. +Our Training Collections provide curated learning paths through our advanced training materials (called [Side Quests](../side_quests/index.md)). This collection covers four essential topics that are frequently used together for building robust and scalable workflows. ## Learning objectives @@ -25,7 +25,7 @@ This collection is designed for users who have completed the basic Nextflow trai **Prerequisites** -- Completion of [Hello Nextflow](../../hello_nextflow/index.md) training or equivalent experience +- Completion of [Hello Nextflow](../hello_nextflow/index.md) training or equivalent experience - Basic familiarity with Nextflow syntax and concepts - Understanding of basic workflow development patterns - Experience with command-line tools @@ -34,10 +34,10 @@ This collection is designed for users who have completed the basic Nextflow trai This collection consists of four Side Quests that cover complementary workflow engineering topics: -1. **[Workflows of Workflows](../../side_quests/workflows_of_workflows)** - Complex workflow architecture and composition -2. **[Testing with nf-test](../../side_quests/nf-test)** - Testing strategies for Nextflow workflows -3. **[Metadata](../../side_quests/metadata)** - Handling metadata for items in Nextflow channels -4. **[Splitting and Grouping](../../side_quests/splitting_and_grouping)** - Advanced data processing patterns +1. **[Workflows of Workflows](../side_quests/workflows_of_workflows/index.md)** - Complex workflow architecture and composition +2. **[Testing with nf-test](../side_quests/nf_test/index.md)** - Testing strategies for Nextflow workflows +3. **[Metadata](../side_quests/metadata/index.md)** - Handling metadata for items in Nextflow channels +4. **[Splitting and Grouping](../side_quests/splitting_and_grouping/index.md)** - Advanced data processing patterns Each Side Quest is self-contained and covers independent concepts, but we recommend completing them in the order listed above for a logical progression through the topics. diff --git a/docs/en/docs/training_collections/index.md b/docs/en/docs/training_collections/index.md index 2acedcab47..b998c6ef07 100644 --- a/docs/en/docs/training_collections/index.md +++ b/docs/en/docs/training_collections/index.md @@ -13,9 +13,9 @@ This section contains curated collections of training modules called [Side Quest Each collection has specific prerequisites documented on its index page. However, most collections assume: - Experience with the command line -- Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../../hello_nextflow/index.md) beginner training course +- Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../hello_nextflow/index.md) beginner training course -For technical requirements and environment setup, see the [Environment Setup](../../envsetup/index.md) mini-course. +For technical requirements and environment setup, see the [Environment Setup](../envsetup/index.md) mini-course. ## Available collections From 81bc393540b636cf01ead6ad65f6547a6e8147e0 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 21:08:40 -0400 Subject: [PATCH 7/8] last links to fix (I live in hope) --- docs/en/docs/hello_nf-core/03_use_module.md | 2 +- docs/en/ui-strings.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/en/docs/hello_nf-core/03_use_module.md b/docs/en/docs/hello_nf-core/03_use_module.md index b01c454ae7..434e82ff64 100644 --- a/docs/en/docs/hello_nf-core/03_use_module.md +++ b/docs/en/docs/hello_nf-core/03_use_module.md @@ -296,7 +296,7 @@ include { FIND_CONCATENATE } from '../modules/nf-core/find/concatenate/main' Note that the nf-core convention is to use uppercase for module names when importing them. -Open up [core-hello/workflows/hello.nf](core-hello/workflows/hello.nf) and make the following substitution: +Open up `core-hello/workflows/hello.nf` and make the following substitution: === "After" diff --git a/docs/en/ui-strings.yml b/docs/en/ui-strings.yml index c5ae3668b4..085b998292 100644 --- a/docs/en/ui-strings.yml +++ b/docs/en/ui-strings.yml @@ -16,7 +16,7 @@ index_page: defaults: technical_requirements: >- You will need a GitHub account OR a local installation of Nextflow. Our training courses are compatible with Nextflow version 25.10.2 or later and require the use of the v2 parser **EXCEPT the Hello nf-core course**, which requires the v1 parser. - See [Environment options](../envsetup/index.md) for more details. + See [Environment options](/envsetup/) for more details. videos: >- Videos are available for each chapter, featuring an instructor working through the exercises. The video for each part of the course is embedded From e9f6eec2c98a40609dfcdcfb78057d2e1b007e04 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 27 Apr 2026 22:09:28 -0400 Subject: [PATCH 8/8] Minor fixes to the training docs Nothing functional, just text, formatting etc --- docs/en/docs/hello_nextflow/01_hello_world.md | 26 +++++++++---------- .../docs/hello_nextflow/02_hello_channels.md | 2 -- 2 files changed, 12 insertions(+), 16 deletions(-) diff --git a/docs/en/docs/hello_nextflow/01_hello_world.md b/docs/en/docs/hello_nextflow/01_hello_world.md index f9fa616ebe..77f1b2828e 100644 --- a/docs/en/docs/hello_nextflow/01_hello_world.md +++ b/docs/en/docs/hello_nextflow/01_hello_world.md @@ -765,19 +765,19 @@ In the process block, make the following code change: === "After" ```groovy title="hello-world.nf" linenums="14" hl_lines="3" - script: - """ - echo '${greeting}' > output.txt - """ + script: + """ + echo '${greeting}' > output.txt + """ ``` === "Before" ```groovy title="hello-world.nf" linenums="14" hl_lines="3" - script: - """ - echo 'Hello World!' > output.txt - """ + script: + """ + echo 'Hello World!' > output.txt + """ ``` The `$` symbol and curly braces (`{ }`) tell Nextflow this is a variable name that needs to be replaced with the actual input value (=interpolated). @@ -809,15 +809,15 @@ In the workflow block, make the following code change: === "After" ```groovy title="hello-world.nf" linenums="23" hl_lines="2" - // emit a greeting - sayHello(params.input) + // emit a greeting + sayHello(params.input) ``` === "Before" ```groovy title="hello-world.nf" linenums="23" hl_lines="2" - // emit a greeting - sayHello() + // emit a greeting + sayHello() ``` This tells Nextflow to run the `sayHello` process on the value provided through the `--input` parameter. @@ -1002,8 +1002,6 @@ Knowing how to launch workflows and retrieve outputs is great, but you'll quickl Here we show you how to use the [`-resume`](https://nextflow.io/docs/latest/cache-and-resume.html) feature for when you need to re-launch the same workflow, how to inspect the log of past executions with [`nextflow log`](https://nextflow.io/docs/latest/reference/cli.html#log), and how to delete older work directories with [`nextflow clean`](https://nextflow.io/docs/latest/reference/cli.html#clean). - - ### 4.1. Re-launch a workflow with `-resume` Sometimes, you're going to want to re-run a pipeline that you've already launched previously without redoing any steps that already completed successfully. diff --git a/docs/en/docs/hello_nextflow/02_hello_channels.md b/docs/en/docs/hello_nextflow/02_hello_channels.md index ae46e392e2..1925752000 100644 --- a/docs/en/docs/hello_nextflow/02_hello_channels.md +++ b/docs/en/docs/hello_nextflow/02_hello_channels.md @@ -603,8 +603,6 @@ Have a look at the `results` directory to see if all the output greetings are th └── output.txt ``` -Yes! And they each have the expected contents. - ??? abstract "File contents" ```console title="Bonjour-output.txt"