From 2adf3705f3406f68de5408a1bc3401b08ecfb8eb Mon Sep 17 00:00:00 2001 From: FriederikeHanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 11:35:34 +0100 Subject: [PATCH 1/7] add extra path for demo run --- docs/hello_nextflow/09_hello_nf-core.md | 15 +++++++++---- docs/hello_nextflow/img/nested.excalidraw.svg | 21 +++++++++++++++++++ .../img/pipeline.excalidraw.svg | 6 +++--- 3 files changed, 35 insertions(+), 7 deletions(-) create mode 100644 docs/hello_nextflow/img/nested.excalidraw.svg diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 2a3c072a..e2f30141 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -36,11 +36,12 @@ So if you want to try out an nf-core pipeline with minimal effort, you can start !!!tip - You can run this from anywhere, but if you feel like being consistent with previous exercises, you can create a `hello-nf-core` directory under `hello-nextflow`. If you were working through Part 7 (Hello nf-test) before this, you may need to go up one level first. + You can run this from anywhere, but if you feel like being consistent with previous exercises, you can create a `nf-core-demo` directory under `hello-nextflow/hello-nf-core`. If you were working through Part 7 (Hello nf-test) before this, you may need to go up one level first. ```bash - mkdir hello-nf-core cd hello-nf-core + mkdir nf-core-demo + cd nf-core-demo ``` Whenever you're ready, run the command: @@ -373,7 +374,7 @@ Instead of having one large monolithic pipeline script, it's broken up into smal - **Subworkflows:** Two or more modules that are packaged together as a mini workflow <figure class="excalidraw"> - --8<-- "docs/nf_develop/img/nested.excalidraw.svg" + --8<-- "docs/hello_nextflow/img/nested.excalidraw.svg" </figure> Within your pipeline repository, `modules` and `subworkflows` are stored within `local` and `nf-core` folders. The `nf-core` folder is for components that have come from the nf-core GitHub repository while the `local` folder is for components that have been developed independently (usually things very specific to a pipeline): @@ -436,6 +437,10 @@ There are several configuration files that are stored in the `conf` folder and a The `nextflow_schema.json` is a file used to store parameter related information including type, description and help text in a machine readable format. The schema is used for various purposes, including automated parameter validation, help text generation, and interactive parameter form rendering in UI interfaces. +#### `assets/schema_input.json` + +The `schema_input.json` is a file used to define the input samplesheet structure. Each column can have a type, pattern, description and help text in a machine readable format. The schema is used for various purposes, including automated validation, and providing helpful error messages. + ### Takeaway You have an example pipeline, and learned about important template files. @@ -1149,6 +1154,8 @@ nextflow run . -profile docker,test --outdir results --input ../data/sequencer_s [2a/a742ae] process > MYORG_MYFIRSTPIPELINE:MYFIRSTPIPELINE:MULTIQC [100%] 1 of 1 ✔ ``` +If you want to learn more about how to fine tune and expand the samplesheet schema further, visit [nf-schema](https://nextflow-io.github.io/nf-schema/2.2/nextflow_schema/sample_sheet_schema_specification/). + ### Takeaway You know how to adapt the samplesheet to add new meta information to your files. @@ -1323,7 +1330,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' and call it on our input data: -```groovy title="workflows/myfirstpipeline.nf" linenums="41" +```groovy title="workflows/myfirstpipeline.nf" linenums="47" FASTQE(ch_samplesheet) ch_versions = ch_versions.mix(FASTQE.out.versions.first()) ``` diff --git a/docs/hello_nextflow/img/nested.excalidraw.svg b/docs/hello_nextflow/img/nested.excalidraw.svg new file mode 100644 index 00000000..49aa78b3 --- /dev/null +++ b/docs/hello_nextflow/img/nested.excalidraw.svg @@ -0,0 +1,21 @@ +<svg version="1.1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1130.729427941043 704.1551513671875" width="1130.729427941043" height="704.1551513671875"> + <!-- svg-source:excalidraw --> + <!-- payload-type:application/vnd.excalidraw+json --><!-- payload-version:2 --><!-- payload-start 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font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> input:</text><text x="0" y="100" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fasta)</text><text x="0" y="125" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="150" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> output:</text><text x="0" y="175" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fai)</text><text x="0" y="200" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="225" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> when:</text><text x="0" y="250" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> task.ext.when == null || task.ext.when</text><text x="0" y="275" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="300" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> script:</text><text x="0" y="325" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> def args = task.ext.args ?: ''</text><text x="0" y="350" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> """</text><text x="0" y="375" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> my-function $args -i $fasta -o $fai</text><text x="0" y="400" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> """ </text><text x="0" y="425" font-family="Virgil, Segoe UI Emoji" font-size="20px" 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payload-end --> + <!-- payload-type:application/vnd.excalidraw+json --><!-- payload-version:2 --><!-- payload-start 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fill="none"></path></g><g transform="translate(277.7147584598731 527.8807247408636) rotate(0 0.186586908905781 15.03209629979898)"><path d="M-4.34 15.56 C-2.92 18.53, -1.2 22.67, 1.1 29.57 M-4.34 15.56 C-2.82 18.53, -1.47 21.83, 1.1 29.57" stroke="#1e1e1e" stroke-width="2" fill="none"></path></g><g transform="translate(277.7147584598731 527.8807247408636) rotate(0 0.186586908905781 15.03209629979898)"><path d="M5.94 15.33 C4.83 18.41, 4.01 22.61, 1.1 29.57 M5.94 15.33 C5.05 18.33, 4.01 21.69, 1.1 29.57" stroke="#1e1e1e" stroke-width="2" fill="none"></path></g></g><mask></mask></svg> \ No newline at end of file From 3938fc92f6c3e7a45343b3e38a98e99b2f04aff8 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 11:41:21 +0100 Subject: [PATCH 2/7] add hint for new window --- docs/hello_nextflow/09_hello_nf-core.md | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index e2f30141..364591e5 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -36,10 +36,9 @@ So if you want to try out an nf-core pipeline with minimal effort, you can start !!!tip - You can run this from anywhere, but if you feel like being consistent with previous exercises, you can create a `nf-core-demo` directory under `hello-nextflow/hello-nf-core`. If you were working through Part 7 (Hello nf-test) before this, you may need to go up one level first. + You can run this from anywhere, but if you feel like being consistent with previous exercises, you can create a `nf-core-demo` directory under `hello-nextflow`. If you were working through Part 7 (Hello nf-test) before this, you may need to go up one level first. ```bash - cd hello-nf-core mkdir nf-core-demo cd nf-core-demo ``` @@ -260,6 +259,22 @@ nf-core --help ### Creating your pipeline +Before we start, let's navigate into the `hello-nf-core` directory: + +``` +cd .. +cd hello-nf-core +``` + +!!! hint "Open a new window in VSCode" + + If you are working with VSCode (for example running the training on GitPod), you can open a new window to reduce visual clutter: + + ```bash + code . + ``` + + Let's start by creating a new pipeline with the `nf-core pipelines create` command: All nf-core pipelines are based on a common template, a standardized pipeline skeleton that can be used to streamline development with shared features and components. From f5eca6467db7bc9e8bfd01f0e7d98add7a3502a4 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 12:13:34 +0100 Subject: [PATCH 3/7] Update docs/hello_nextflow/09_hello_nf-core.md Co-authored-by: Christopher Hakkaart <chris.hakkaart@seqera.io> --- docs/hello_nextflow/09_hello_nf-core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 364591e5..a186daa0 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -268,7 +268,7 @@ cd hello-nf-core !!! hint "Open a new window in VSCode" - If you are working with VSCode (for example running the training on GitPod), you can open a new window to reduce visual clutter: + If you are working with VS Code you can open a new window to reduce visual clutter: ```bash code . From a3ff85f221842ab0b95f4487055fdf9b93eb563b Mon Sep 17 00:00:00 2001 From: Friederike Hanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 12:13:43 +0100 Subject: [PATCH 4/7] Update docs/hello_nextflow/09_hello_nf-core.md Co-authored-by: Christopher Hakkaart <chris.hakkaart@seqera.io> --- docs/hello_nextflow/09_hello_nf-core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index a186daa0..a67c6d7a 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -1169,7 +1169,7 @@ nextflow run . -profile docker,test --outdir results --input ../data/sequencer_s [2a/a742ae] process > MYORG_MYFIRSTPIPELINE:MYFIRSTPIPELINE:MULTIQC [100%] 1 of 1 ✔ ``` -If you want to learn more about how to fine tune and expand the samplesheet schema further, visit [nf-schema](https://nextflow-io.github.io/nf-schema/2.2/nextflow_schema/sample_sheet_schema_specification/). +If you want to learn more about how to fine tune and develop the samplesheet schema further, visit [nf-schema](https://nextflow-io.github.io/nf-schema/2.2/nextflow_schema/sample_sheet_schema_specification/). ### Takeaway From 02ea3ebc521d0e2da18ee69d845c04b724c215d0 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 12:13:49 +0100 Subject: [PATCH 5/7] Update docs/hello_nextflow/09_hello_nf-core.md Co-authored-by: Christopher Hakkaart <chris.hakkaart@seqera.io> --- docs/hello_nextflow/09_hello_nf-core.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index a67c6d7a..577dde3b 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -273,8 +273,6 @@ cd hello-nf-core ```bash code . ``` - - Let's start by creating a new pipeline with the `nf-core pipelines create` command: All nf-core pipelines are based on a common template, a standardized pipeline skeleton that can be used to streamline development with shared features and components. From 3ecf637fa2285de44d1fecc5621c309a663b11ec Mon Sep 17 00:00:00 2001 From: FriederikeHanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 12:45:17 +0100 Subject: [PATCH 6/7] linting --- docs/hello_nextflow/09_hello_nf-core.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 577dde3b..0f1d2402 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -273,6 +273,7 @@ cd hello-nf-core ```bash code . ``` + Let's start by creating a new pipeline with the `nf-core pipelines create` command: All nf-core pipelines are based on a common template, a standardized pipeline skeleton that can be used to streamline development with shared features and components. @@ -452,7 +453,7 @@ The `nextflow_schema.json` is a file used to store parameter related information #### `assets/schema_input.json` -The `schema_input.json` is a file used to define the input samplesheet structure. Each column can have a type, pattern, description and help text in a machine readable format. The schema is used for various purposes, including automated validation, and providing helpful error messages. +The `schema_input.json` is a file used to define the input samplesheet structure. Each column can have a type, pattern, description and help text in a machine readable format. The schema is used for various purposes, including automated validation, and providing helpful error messages. ### Takeaway From 50cc8d6dadae930f0c88c3c3fd6e90393d903454 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen <friederike.hanssen@seqera.io> Date: Thu, 21 Nov 2024 12:45:53 +0100 Subject: [PATCH 7/7] image --- docs/hello_nextflow/img/nested.excalidraw.svg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/hello_nextflow/img/nested.excalidraw.svg b/docs/hello_nextflow/img/nested.excalidraw.svg index 49aa78b3..277b2407 100644 --- a/docs/hello_nextflow/img/nested.excalidraw.svg +++ b/docs/hello_nextflow/img/nested.excalidraw.svg @@ -1,6 +1,6 @@ <svg version="1.1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1130.729427941043 704.1551513671875" width="1130.729427941043" height="704.1551513671875"> <!-- svg-source:excalidraw --> - <!-- payload-type:application/vnd.excalidraw+json --><!-- payload-version:2 --><!-- payload-start 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<!-- payload-end --> + <!-- payload-type:application/vnd.excalidraw+json --><!-- payload-version:2 --><!-- payload-start 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text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> label "process low"</text><text x="0" y="50" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="75" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> input:</text><text x="0" y="100" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fasta)</text><text x="0" y="125" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="150" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> output:</text><text x="0" y="175" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fai)</text><text x="0" y="200" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="225" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> when:</text><text x="0" y="250" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> task.ext.when == null || task.ext.when</text><text x="0" y="275" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="300" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> script:</text><text x="0" y="325" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> def args = task.ext.args ?: ''</text><text x="0" y="350" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> """</text><text x="0" y="375" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" 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UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fasta)</text><text x="0" y="125" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="150" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> output:</text><text x="0" y="175" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> tuple val(meta), path(fai)</text><text x="0" y="200" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="225" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> when:</text><text x="0" y="250" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> task.ext.when == null || task.ext.when</text><text x="0" y="275" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> </text><text x="0" y="300" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> script:</text><text x="0" y="325" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> def args = task.ext.args ?: ''</text><text x="0" y="350" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> """</text><text x="0" y="375" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> my-function $args -i $fasta -o $fai</text><text x="0" y="400" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge"> """ </text><text x="0" y="425" font-family="Virgil, Segoe UI Emoji" font-size="20px" fill="#000000" text-anchor="start" style="white-space: pre;" direction="ltr" dominant-baseline="text-before-edge">}</text></g></svg> \ No newline at end of file