From 2adf3705f3406f68de5408a1bc3401b08ecfb8eb Mon Sep 17 00:00:00 2001 From: FriederikeHanssen 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
- --8<-- "docs/nf_develop/img/nested.excalidraw.svg" + --8<-- "docs/hello_nextflow/img/nested.excalidraw.svg"
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 @@ + + + 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 + + + + + InputsMODULE_1SUBWORKFLOW_1OutputsMODULE_4MODULE_2MODULE_3WORKFLOWSUBWORKFLOW_1MODULE_2modules.configtool argumentspublishingoutput namesbase.configcompute resourceserror strategiesprocess MODULE_2 { label "process low" input: tuple val(meta), path(fasta) output: tuple val(meta), path(fai) when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ my-function $args -i $fasta -o $fai """ } \ No newline at end of file diff --git a/docs/hello_nextflow/img/pipeline.excalidraw.svg b/docs/hello_nextflow/img/pipeline.excalidraw.svg index ae940126..bcf2d6e5 100644 --- a/docs/hello_nextflow/img/pipeline.excalidraw.svg +++ b/docs/hello_nextflow/img/pipeline.excalidraw.svg @@ -1,6 +1,6 @@ - + - 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199UT83q+OJ4XHUwMDEyXHUwMDA0lMi+oGNfXHUwMDA04KC3fLJ7XHUwMDEwtlx1MDAwNXFqs+rAkrBcdTAwMTDv6lv67TL+5JEkiiioqMHahn15kVx1MDAxNtVcdTAwMTZcdTAwMDXghVx1MDAwNOFcdTAwMDSrabtcdTAwMDPul1x1MDAxYlpFt2/l+f1cdTAwMGah/Fx1MDAxMClcdTAwMTch2bZiYmnE7P134cnt/nX9tt9w752aPD0+q6v1zSVcdTAwMDeyoFxiKDKWXHUwMDEwoXCmmMjgWFx1MDAwMMxccvhPiFx1MDAxZoV619tmxTAmtl2eXHUwMDE4MFk2ScdUTqGqhFx1MDAwMb84UPgoqqSpwIH+XFy2XHUwMDBmlvuNbP946PV6bns1Lvt+LOEvXHUwMDE4ejbO/65qMytOyVOqJbOsd2Zccu7uutH15daoczqMXHUwMDBlauzB7V2dOMutwUIrpIjUnErrXHUwMDA2Mp094IEgXHUwMDFl0kJpYZXDiHdV6Ip1mFxuXHUwMDA0tFx1MDAwZlx1MDAxNFDb5KGWiVx1MDAxNFx1MDAxM75IXHUwMDAzJYRonVx1MDAxYqkomXZGXHUwMDEwpmjB1UJeXHUwMDE3/Vx1MDAxNbxcdTAwMTEsTlx1MDAxMZilZFx1MDAxMElgNrs3OjNkq1U/3W24R1x1MDAxNzT8rNb3XHUwMDFiX7vLjWVcdGTakmUh7CtcdTAwMTnSZChcdTAwMWRcdTAwMDRdjEFcXM8h3sWCmXdVl1xusWxcdTAwMDRittitiIDRcKrHdVx1MDAwZXdEbY+dUKaCVtRf1lx1MDAxYlx1MDAwNYG/+oLtj3VGuSN/gC8qXHUwMDBlJjmYPVx1MDAwM1HU7NXhq7Pdw85N+0J06u7+2Tk9iNxauNzqK4RBNsulXHUwMDE5XHUwMDE4cZN+k+npL1x1MDAxN0ikTdxNXHUwMDA00OTmXY1PxZ7ItldxJlx1MDAxOfhcdTAwMTjKwDHme1wiSTnmQIpiT5SKa1+CSVx05kVw8X/LiyCYLsQy4FhcdTAwMTlK53gxqfxvISwnlo1cdTAwMDHDx4VmTCus8WRYXHUwMDA1tFx1MDAxYimN4aQhQJ/xYjyRXHUwMDA29sWMiamZsT18b1wiRty+biy4XvhcdTAwMWK9Y6B/eHdcdTAwMDCz3dM/zdHFnGdcdTAwMTVA7IZcdTAwMWbr53JcdTAwMDeuws1cdTAwMTWXXHUwMDFkdGGVlWKu41eC5nhruLQxbilcdTAwMWIkpOBcYkJTIFqc8oyDk4QjYFlcdTAwMTScm01OZ4WqxiZgxFx1MDAxNFxmz4DraZLfXHUwMDA2yezfbuFgl8CGXHSjTF6xgUqIb1Uyt+UpNlxine4qq77YMHMtXHUwMDEzqIjCNlCBgEbz+OXQ1FVP1Vx1MDAwNo2MtMTa1m7sX3qYnvtM9dXyvuBcdJmA91DCXHUwMDE1sCRcdCijeX8riFiWRDVsvqXbXFxMyfQrlTlcbvFuP1NIT562kv62PiR+/pozXHUwMDE4XHUwMDFjRYC48WZcdTAwMDDyvfazXHUwMDBiSCa5due59+vFarnyvJxrT8ZcdTAwMTdcdTAwMWX2Y+XHf1x1MDAwMUBQXHUwMDFiXHUwMDFlIn0= - samplesheet.csvMULTIQCsample,fastq_1,fastq_2SAMPLE1_PE,sample1_R1.fastq.gz,sample1_R2.fastq.gzSAMPLE2_PE,sample2_R1.fastq.gz,sample2_R2.fastq.gzSAMPLE3_SE,sample1_R1.fastq.gz,SAMPLE3_SE,sample2_R1.fastq.gz,multiqc_report.htmlSEQTK_TRIMTrimmed fastqTool versionfastq files \ No newline at end of file + samplesheet.csvMULTIQCsample,fastq_1,fastq_2SAMPLE1_PE,sample1_R1.fastq.gz,sample1_R2.fastq.gzSAMPLE2_PE,sample2_R1.fastq.gz,sample2_R2.fastq.gzSAMPLE3_SE,sample1_R1.fastq.gz,SAMPLE3_SE,sample2_R1.fastq.gz,multiqc_report.htmlSEQTK_TRIMTrimmed fastqTool versionfastq files \ No newline at end of file From 3938fc92f6c3e7a45343b3e38a98e99b2f04aff8 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen 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 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 --- 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 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 --- 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 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 --- 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 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 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 @@ - 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7px2XHUwMDEwXHUwMDA2SrBWb2BcdTAwMDeZLLHc6znBO3+LleVw6L19bHXsoVlYVlIjXHUwMDEy0633XHUwMDAyXHUwMDA0XHUwMDFiaTCZ31xyN5uz5Fx1MDAxNeVcdTAwMTKjXHUwMDA0cydnXHUwMDA0Kc7JtNs7c0NcbuHImuKZXHUwMDA2NquT/XJxoFx1MDAwYiWNveGHplAsOb+VXHUwMDAz0t9cZucvQXz8h4RcdTAwMGXybJE+O+mdpisyRGGQ5JiZX5HRte3Vg9rRaLS//rQ67lxcle+rg5u8411cdTAwMTONlGSRVFx1MDAwNd9bJ1x1MDAxOJJG0eVG01x1MDAxMEVcdTAwMTEnkYiZqWzeqCdxXHUwMDEyTsOVWJLKkiff3GwnXHUwMDAwT42gJ1b4NYotkI2+5ZLS+eF+dbVxdE5aklSqo+P1/C9gXHUwMDBlmriKpHz71keuXHUwMDExjyXi5mdcdTAwMDHD5Fx0q3b/9Es4TdpcdTAwMTIhXHUwMDA3VXT1gjJLXHUwMDE55fPrVO2T1dv6vbOhvIdWc7N2sHPxedXJ/eJcdTAwMTUgViUlgFxijZYua1x0XHUwMDA0XHUwMDFhsonKdLM0Klx1MDAxMMyYgVx1MDAwNfJDJa2rw8b1ff/s6rHp3p6vXq9uj9new3yS1sdZ37tdajyy4oHqdbfrJbO309rgn8Q71dReZCn6QyQ4mq1cdTAwMDSXRj0kSVxyTrGDzfVcdTAwMDJZsFvjhji/cuRcdTAwMTU+Kt3X929cdTAwMWaeXHUwMDFlP/HcXHUwMDEzXHUwMDBmLlx1MDAxMaNcdGUmQHDTUaqyXGbywWz2mKSRJ80gIIxzXHUwMDBl8mSIXHUwMDE3/kT047CHtXNd+rT71K/hMd+/LJW38fumXHUwMDFm7IfQXHUwMDBmli39SHVjaZXqvpeSUmnoXHUwMDAyXqzZqyqnXHUwMDE0xGBia55JJbHhtrzZtFx1MDAxMGJAXHUwMDAxlEuOccMghDBlrMtcdTAwMDTIXGJcdTAwMTCThEBNrpAgRiTFznCiQSiRyyl5lnN//WyJtzCVv061XHUwMDE20prJXHUwMDA0qCrahPK6XHUwMDAzx9XrXHUwMDE4x956Lo/VbFx1MDAxNlqY9qNcdTAwMDG8NNOK+b4ykuRHo0hcdTAwMWFD330+fTF9fdsjtLKDb/pcdTAwMTD+nSVVM7BcdTAwMDRcYqZcdTAwMGLEJM3maTmlatpcdTAwMThklLbrR2BcdTAwMTMuSPZcdTAwMWOTZJBcdTAwMTZiufVBsM3qJ4JcYiOJsFksXHTSkYppfpMgJGV5j8ZLqVOXc6I2N1x1MDAxOVx1MDAwMSqigTwwJiSzleVk3O9ccjTNqDlcboQsM6dlya7wlGVmj2CBLUhaUs01Kt1cXMM4UUTSXHUwMDA1vGPlS13qt/u7q2uN1d1ubcu9Wyub/JFcdTAwMTaOXHUwMDE0XHUwMDAxLGqjMVx1MDAwM4UrgKRfM5ZcdTAwMDObUlxuuJjNalx1MDAwMUVoWn5iXHUwMDAywcBoyTWebs2+lIdGsFxijFD62Vx1MDAxNFx1MDAxYTxqljlcdTAwMDfkPq6Voks35+RHsXlcctV/W8Um/tQsXHUwMDE0m9TccJ7q1YKVzEBcdTAwMDSZ3yUw3lx1MDAxM1x1MDAwN6X+1vruw2jPeVSfXHUwMDFlq63ju/yhNOLDJoDaaYP8c1xyZ4l41K+cOeePI49hg6Lyxos9hFx1MDAwMkVcdTAwMTGZXHUwMDAwMLeM/mdLJZ26OpjaXHUwMDA1eWxqXHUwMDFhOEmt60BgRWtcdTAwMWLpO79Z81LWV51cdTAwMWHmtVtYno8lZ/Nh4zz/Plx1MDAxMWBmXCJm1KSYg0a4ZJ9cYkaxXHUwMDEwl4B/Mr/mYGJcdTAwMDaPtD6+nMbPUiPVXCKl0f80OI7NtT3Cs5yR2KxnlOTFoKJqoVx1MDAxN0iiPTsqnrDi6KF3zHGpze+v7m9X1/JcdTAwMDfpmWKzXHUwMDAyqolcdTAwMDVTWlHmx45OI1x1MDAxZNR3zrHAwujp1nzk11JcZkK2rXL0V37tO8+vTbWhhWO5Y65FyVx1MDAwNKHz8+DZbuXcXHUwMDAwNu5cdTAwMTjARlNMbTlhTqdLs9jiXG7QgG1cdTAwMTS+XHUwMDAxXHUwMDExXGIvXHUwMDExokhryTCoLEAqXHUwMDE4KKxcdMXsqbRcdTAwMTGr3JZyYFxua1x1MDAxMSok8ypnS1xmUoUhueTPS5ezv9t/YC32QPOIxpRJg42gKm5sM0hcdTAwMDMlpYTDJZpy8b6TTNLXnT3iK25BWWFmUFx1MDAxZmEsPdeEXHUwMDEyqrAg8zsma6ObRvdpg9844un09Ob2qtfcK+ed/oA0TZHy0zQ1kFx1MDAxZkMjJb6ZhlZcdTAwMWNcdTAwMWMy0rNcZqu9WVuCkphcdTAwMTObzU2TNtPgkqKXXGJaXHUwMDFl2ZbmVWQw0MhcdTAwMDXPIO4h81x1MDAwNH+xdWlqt20+LFxynU9cdTAwMGbm8vH2plx1MDAxY840i/HLScvscIiLxkiu8Vx1MDAwZcbNcW1vd3iw9ri6kV1AvFIsVPr1O+NcdTAwMTPTlPFwleNYiVxyS1x1MDAxZKRYwJR2ddfs3Fxy1sXZ/oVQx737JqlcdTAwMWPmPrrWXHUwMDE4iVwi9Vx1MDAxNF9jw2MpXHUwMDFhme+noWzC5XRcXO9cdTAwMDR00K/IZmyvxTRsrlx1MDAwNFxi53ktIJtFLuvPposnzLQ9iq+TvCB3TTWM69RoeZsrKqVcXEBcdTAwMTFcdTAwMWbe7X4+fqrfn+DTT4PtXHUwMDFhPVlvXHUwMDFl5j/gx9iQeJpcdTAwMDBobTV2vNSC88DSp1x1MDAxZlx1MDAxMLKQXHUwMDEzZKIx9C+ANlJcYs1kXHUwMDE22nbmeNbEZJKb/rPhOTrT9lxiz3FGeCbpji5pqzJcdTAwMTOzgJ5+w3ZbXHUwMDE3+43K9onccVx1MDAxZlx1MDAwZXdEq6dcdTAwMWbzjmdcdTAwMDKQRVx0ni5uUGTvmaz18lx1MDAwNDFY2GI/SfWtMONcXEmq8qp+/1x1MDAwNeH41SR89WRqXHUwMDE3XHUwMDA0bqpJfEYkicaGWMK6QLljuVFr4Z2jYvn8ZPfiorl3enWYw33qZprEXHUwMDAxI1x1MDAwNFx0TGUsNM3nzjY6U9iqS1FcdTAwMWX545OCqJRYXHUwMDExQ364NfybUPynz675iiVKRc++4lRrW4JFzW+H+txsXXSa62J4pzuVY3PbviRbWykojaBtXHUwMDFhozRyfslWKIAqV0ZcdTAwMTElXGaZtkJJaCVcXDHAdHSnt1xiLIlj/307LClWoFxiRfTwgPFqZG1kScKz3VxukEtcdTAwMWOymv9cdTAwMTSGp1fmkyFF+CY+XHUwMDE2LspcdTAwMTDdwMxcdTAwMTajw2ZcdTAwMDGAnI1Le5s3W9W141HrfMO7XHUwMDE5V9rXKudcdTAwMDAhmCNb5Fx1MDAxMqCQXHUwMDA0XHUwMDEwLVx1MDAxMFx1MDAxNoqb163xllx1MDAwNlx1MDAxMMJcdTAwMThcdTAwMTKg3FxuJkgySFx1MDAxMsRSX1xy5qE+//SMq92tXHUwMDBlW85cdTAwMDBcdTAwMDHXqbn1t2Vfac9eZoooIambaijMXHLoqPNLmeTpptjYXCKtR+du1HBcdTAwMGbOXHUwMDFipXrpMO/wXHUwMDA0cY5cdTAwMWEjMU/iX4ppRFx1MDAxOaPx8lx1MDAxZpnDkytEmNGS4uei/Fx0gVx1MDAxNlx00ZFcdTAwMDKwoUAo/vNcdTAwMDDU63ZbhXK/PvT79nunN7xtuYNcdTAwMDYokr93un4hrEJcdTAwMDde9o1LcC3eq7lALb9HMlxy2feTdiawm2fOb8tV3jbfL4/WyuUr5/i02lg73n5Iq9SVXHUwMDE3bDNcdTAwMGXjavc0oZrTXHUwMDA02ZQgbneqMdzQfMqmdlx1MDAxN2RMlFJcdTAwMTkw4MyF0+V6L99GOFxyXHUwMDE1lokqb1RcdTAwMTKbkrLA/lx1MDAwMJ93+reV8d7O/uYpvTpi413eXHUwMDFi51x1MDAxZCGSIyOkwsZcbuLKTIdcdTAwMTlK6/EwQr1cdTAwMDH3w1x1MDAwMllyZJgy2t/Ralx1MDAxZfHUryqsSFx1MDAxNqrbe+F+ljf8XHUwMDEw2TTxwUtcdTAwMTVMeSo2XHUwMDE5XGKlNsZwfsm0t3Z/4Vxma71m/bPwSqwu1k6OT/KOTZuLY4D+YyNcdTAwMTMkU45cdTAwMTHIpXZcdTAwMWOWjU3t571rLMzzXHUwMDFl2Fx02FxmTcUkc07a7HVcdTAwMWPS7n96cFa6bVx1MDAxMPScQt9cdTAwMTl0h/2KXHUwMDAzcqBcdTAwMDOcr1+AKYGO1d23lkpcdTAwMTfq0FxcYOZsJphTw4VJ+t6NxG5IoDhfIE5otl0sn3AmXG6DnCek0TxcdTAwMDHOUtpcdTAwMTg6Y2t1fKVQ9PfC2Vx1MDAwMMfnmtjtXHUwMDBliD/wXHRcdTAwMTKpQSRcdTAwMWG4NFx0XHUwMDFkksZuq7xcdTAwMTRr6Xf5KVx1MDAwNSaChlx1MDAxNOHs8+5nm+dcdTAwMGJTwcB2Q1x0RbmwmVx1MDAxMCDTxPd4XHUwMDA2jUAqu9ltclx1MDAwMY+5opNnx61Od4hTrqUtJkKVjfTGXHRbYXNEbe0pKp+rbdD3XHUwMDFknixcdTAwMDTSkV3p7FEk8qVs4Ne+IFx1MDAxNSj+11x1MDAwNFx1MDAxOFx0vudD+PfiJHLGToJUcFx1MDAwNvrIXCLbYs7UzvJJXCK5wFxiZFx1MDAwNml3m1RaTGdUSGn3XHUwMDExl0Jxuys6I+n7JH0vhVx1MDAwNHnHJpGC7MBsdZREnVx1MDAxZOCLXHUwMDEz85VcdJWcS05CZVx1MDAxZfJFIVx1MDAwM1x1MDAxNS97XG4520hcdTAwMTRcIkhAIGGypbZcdTAwMTkykuOkaktcdTAwMDZhmGjfLFx1MDAwYugjOG6tyJZGgjgtXHUwMDE4dMpcdTAwMTbsXHUwMDEzUmBcdTAwMTWn2YQh6DKB/6m/XHUwMDAyXHUwMDEziqa8J1xuWfxuXHUwMDEyWUyFit9cdTAwMWGgZEFcdTAwMWGZqlx1MDAxM2Kd6k2kmFx1MDAxMKb5XHUwMDAyXHUwMDE1LTfv2qOTU+Lee9fDo7bzeLpT2bhIIZE5XG5nY1xuXHTDJdFAL1x1MDAxOVxy7Vx1MDAxN/dcdTAwMWPWplx1MDAwMVo8blDMeltwLJFcdTAwMTRGUfOyPXBcdTAwMTKRjGuFXFzajVx1MDAwYlhcdTAwMDa08Vt1Qlx1MDAwMLhcdTAwMTLim7K9v0kn7PW7oHdcclxur6EphT9+79hcdTAwMGJa5VunVfh90t7qPvy+8tz0/NPtgOr26/Nnb9hrOYVRufXPtuOV//Wx0Ct7jX/WgNaU/1x1MDAxNb7n2dPwlZvcqVuA0nRebyhcdTAwMGaaXGK6jey5wm+/+YNS+N//plx1MDAxYsI3XHUwMDBmKn239/q8qlOzXHUwMDFlkEHht+BcdTAwMDb/73//WvjHP15uW/H/+Z/bj8XasFPxXHUwMDAww4W/+1x1MDAxN1x1MDAxNt3C3/2XKlx1MDAxNLv2k1x1MDAxYr5cdFx1MDAxZfnlbbXnv6ZuKVM3n53h1dDw4YX5rJR7vVx1MDAxM1x1MDAwZqA84fVAO9zqXHUwMDBiXHUwMDFlg3lcXFx1MDAxObnOw2qcmv2t5lx1MDAxZtZcdOFzXHUwMDFkS95cdTAwMWRfyPry4cv/XHUwMDAxj/HTICJ9 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eyJ2ZXJzaW9uIjoiMSIsImVuY29kaW5nIjoiYnN0cmluZyIsImNvbXByZXNzZWQiOnRydWUsImVuY29kZWQiOiJ4nO1d+W/bOFx1MDAxNv69f4WRXWB3gZrD+1x1MDAxOGCwcM7mTpo7O4tAsWVb8Vx1MDAxOV9xMtv/fVx1MDAxZpXEknW4diunSmfUmcRcdTAwMTEli1wi+b33vYPkXHUwMDFmXHUwMDFmXG6FlcFj1135tbDijstO06v0nIeVj/b8yO31vU5cdTAwMWKKqP93vzPslf0r64NBt//rL7+0nF7DXHUwMDFkdJtO2UUjrz90mv3BsOJ1ULnT+sVcdTAwMWK4rf6/7c9cdTAwMDOn5f7W7bQqg1x1MDAxZVxuXHUwMDFlUnQr3qDTe36W23RbbnvQh2//XHUwMDBm/F0o/OH/XGbVrueWXHUwMDA3TrvWdP1cdTAwMWL8oqCCgrDo2YNO26+s5IxcdTAwMTkq8KTc66/D01x1MDAwNm5cdTAwMDVcbqtQYzcosadWdneL2z23+nB/OX6q7DZHh3ebXHUwMDE3x8FDq16zeTJ4bD43hFOuXHUwMDBme6Eq9Vx1MDAwN71Ow73wKoM6lJPI+cl9/Vx1MDAwZbRBcFevM6zV226/P3VPp+uUvcGjPYeD6j+3wa+F4MxcdTAwMTj+4kpcIo0pVppyhVx1MDAxNVx1MDAwZZrDv19cdESVYpwpXHUwMDExqdJap1x0fVx1MDAwMFX6XHUwMDFi9o+gUrdOuVGDmrUrk2tcdTAwMDY9p93vOj3oqeC6h5eXpZwggyXl5uVQk0vqrlerXHUwMDBm4Fx1MDAxYUZcdTAwMTjiXHUwMDA0XHUwMDEzIWmoXCKu31x1MDAxN5pTbFxmx8Ft9und7Yo/KP5cdTAwMWJ0QFx1MDAwZobTtr2jPWw2w23Yrry04evgXHSGXHUwMDBmeznzJXg9e/1GdNiFh15oTJRcdTAwMGVEsXF4/aD2N5lsPcLoXHUwMDEw46D/psap0+t1XHUwMDFlViYlX14+XHUwMDA19Vx1MDAxZnYrzvPoI4pRorlcdTAwMTGGSj0pb3rtRvTlmp1yI1x1MDAxOLBcdTAwMWZCb7JcdTAwMThOmJRpOIFeUZJKXCL03EhZZfWdnfFcdTAwMDE93z7db581XHUwMDBlz9bvrz7lXHUwMDFkKYJypElo+NnbKFWIcL1UfFx1MDAxMC1cdTAwMTFjwjD1glx1MDAxMJ6AXHUwMDBmilx1MDAwMMAwKFRcZlx1MDAxZVx1MDAwNO4nlEpmcoiPzVvBXHUwMDBmn8pKP+5cdTAwMTdP1uut872b83pm+IDe0eJN8KGYSMNcdTAwMDc1hGHNQ1x1MDAwMPpcdTAwMWE8XHUwMDBlnjpmZK5ddnbF2+t7o1x1MDAwZX/wxu9cdTAwMDFcdTAwMWXG1yBRjDAsXHUwMDEwI9pcdTAwMWbBy0RcdKgq/+HP34RlXHUwMDFjJYojrjGX+lx1MDAxNUkxrFCOOeeYsVx1MDAxY2LlXHUwMDBlP1x1MDAxZVx1MDAxZPVH59f7dG/M9ryn2+7R+XxY+Tjre3dcdTAwMGW3qlx1MDAxZGdt/Lnal/2z895lj5/084nBgTtcdTAwMWUkwY+nqyeqMVx1MDAxM0TTudHHzM5We9vUXHUwMDBlr/eqzY7TlFxyfdrIPfq0RpTgKYT5d1KDgNuFIZk18CRDklx1MDAxOMM41nRcdTAwMWH8XHUwMDEz3CVwNqOoXHUwMDAxgp1cdTAwMDFnmyp4x8oneOdOe3DiPfmDXHUwMDE3T53ddFpe83FqkPiIgFxubre7w0GAWv98qenVLDpWmm51XHUwMDFhNlx1MDAwM1x1MDAwZoypSfGg01xySsvwXHUwMDFjx2u7vXird3pezWs7zdOUZ8I7up9e+5ygUK/fOn3XlvpyeibCn1x1MDAxYjpcdTAwMDHihChcdTAwMWM9/YpxpohQXHUwMDE0L1x1MDAwMPLZXZ9TkEuKXHUwMDExh1x1MDAxN+VcXGhCcMC3/dtcdTAwMDWwRF+3LVHHXCJhNJZcdTAwMDKDQIVcdTAwMWZcdDxUgjUpVVwiXHLVxID9hkVQkqFqpV9XrUvBan/g9Fx1MDAwNqteu+K1a9NcdTAwMTV7cUxsz6FTfHSXh7aWXHUwMDE4XHUwMDAx94BcdTAwMWVmmmrb1vAhdFXN6dp3RcDmrSFcdTAwMWN7Z7dd+Xpd8PUuuTy6PGvi9ilcdTAwMTl6/JLXusXkulx1MDAxMJDmXGZsOyOtXHUwMDA3QFx1MDAxMVx1MDAxNauLRlx1MDAwMoBp+ztWmabTXHUwMDFmrHVaLW9cdTAwMDBtfdTx2oNom/qNV7KAr7tOrMPhZcJlUcnQtd84LeKDT4VcdTAwMDA5/lx1MDAxZpPP//2YeHXawLZHMKSDb/lcdTAwMTD+vShZYTLV51x1MDAwNF0vwIqj89tcbrN7M6eCTEiCtHX5RIxpRpBcXLqdgMFiXHUwMDA3vsInjGUuvlwiJVxiXmBT75SvzDRcdTAwMDC+w7DIXHUwMDFkXHUwMDBm2j9cXD/b27ghb8uE4k9dKlx1MDAxN5KaRM9OzFx1MDAxZEBcdTAwMWZThvP5udDs7s+pXGKRRCFccu8pXHT8MzpcIkikXHUwMDAyosStMJWMcSVYpF5cdTAwMTk6r1x1MDAxMbS2kEYx6yZcdTAwMTdUJTivqUJcbipKKGHSalx1MDAxOVx1MDAxMoj3id9BXHUwMDE4XGY2nPkzkqO5XHRJXHUwMDEx2Fx1MDAxMWZcdTAwMThsR2H5XHUwMDBmXHUwMDA2faFMnJNcdTAwMTCMgKtcdTAwMTAoJH7nU/NtRGm2XHUwMDFibpq0Kes2klpcYmEokDaSVCkgSoJcdTAwMTKluObCXGL+rlx0U/qw90tjXHUwMDAzfkHq5MvHXHUwMDA0wVx1MDAwN22bJvg40WBbcDw/ddpcdTAwMTifN2qyf1Jxe1x1MDAwZrWrddW/vTajvMs9RTiaMq+ePaxcdTAwMTRxJaeDY1x1MDAxOVx1MDAwYjpcdTAwMDHylkg+RdrCjlUplZFJdp8xxrqHllx1MDAxMp3LiWSLwjClJGOAT5Vliu6EvrZHMdTNXHUwMDE5XHUwMDAxmlNcdTAwMWQ9O1x1MDAwMTRwbpAr88ffXHUwMDA3e6O68CpdXbpaOy02TF/e47384zkgaj6UNUbW+F+mx5ZLJOh0TD9cYiRcdTAwMWE0bZi9wlgwXHUwMDAzSpXyv3D8fnBcdTAwMWPvaHu8dvGCXHUwMDEwnlx1MDAxZP9cZrV/ND9AY2w4W0QzX6zSs119uXt5V1mvtGulvf7n4lXukaxcdTAwMDRYJFx0MVx1MDAxOIpcdTAwMDVYI0JcdTAwMTFtXGYn0Fx1MDAwZTpSp1xmrVx1MDAxMUqQxFwiiHAmWSNUW1x1MDAxYVx1MDAxZGTcXHUwMDA017xgXVx1MDAxMeuFYUuxReaIgf7waFwiXHJcdTAwMDWGY8ku0C5cdTAwMDaMyvmTXURnPCZcdTAwMWKVq/LeSbNxU1k/uiiZh7xcdTAwMGZmMJpcdTAwMTAz03ktvnpiXHUwMDE0xdKwsvbQKVx1MDAwMlx1MDAwNpUxVFxi5uNJJ1xm4lx1MDAwNFx1MDAwNSW5L+qW7qLLj7Pr5Gz14vDz7ube4cVbe7xSXHUwMDFlnYXba6aikSRd0XBOYNxcdTAwMDBrnFx1MDAxYpv1i7N9c1ZcdTAwMWaMyj06dq52bj+NTof5x6ZcdTAwMDC1jomihFx1MDAxOFx1MDAxMtarjz6jVsgyd2K4n1x1MDAxMWZcIvXKNuOG+EbCS8ZN4GVcdTAwMGLnpYloWsAkIKi5olxmqzzm2nxHTszHWd+73HzQTLVjuveZzchcdTAwMDWVXHUwMDEyM830/Fxcb3ZL51x1MDAxNIKSaGQopoRhro1cYqVcdTAwMWU/23DShnE5XHUwMDE0aN9e5kvDoDVcdTAwMTaVJFx1MDAwNFNBJaagsZNsOm4jxlx1MDAwNP6TXHUwMDE4K1x1MDAxZIp4vUJRXHUwMDAxRZfSkKVAMSfG3Te7eZ9cdTAwMWS4XHUwMDEygSUloZGgXHUwMDE1rVx1MDAwYiR0wZR/XHUwMDFheLVSoIM4dFx1MDAwYrCluJt3Lt/zbMU0qZRNPpbCaMqElGCgs4RaQaVcYlxcXCJcZlx1MDAxMWBcdTAwMThwo6CGsUq9J9/zjDFvj9hoXHUwMDBmvu9D+PfCcs/o1Fx1MDAwNCSiJTSy1ixA+tfk3mxNkFe5Ryny81JcdTAwMDSl1ID2nqZcdTAwMWVSIaFcdTAwMTSVgjFcIlx1MDAxOVle1Fxy2zxeeFx1MDAwNsU2wMdkKPMrLPVcZjWUg01urO8qTkCALlxuaWMyOZR6kmlcdTAwMTEo0eyl3naj0TvZLO2fXHUwMDFk9Gt3bKcmqnfyU1jAhIWagvpYXHUwMDBmXHUwMDA2Y8A9RdDYhVB0S0Of2ylEIIdcYtUk9vZzib09soZcdTAwMDdYPLLPa/y67lx1MDAxZK+v3Vx1MDAxY2yk1FxuJJ/EnGJlO9FcYlx1MDAxNquURtCIQJOJ0bb7pX7nUi9tyNsjNthcdTAwMTdcdTAwMTR6qYnVJlXmSZC+SqtcdTAwMDXcerN7N6dcIk9og2hs3o8gXHUwMDA0XHUwMDA2IFx1MDAxN2yZfnqNkVx1MDAxMFx1MDAwNtQ1xlx1MDAwMqTunH5cdTAwMTBcdTAwMDZGsFZv4Fx1MDAwN5lcZrHc2znBO3+Ll+VwOHj73OrYQ7PwrKRmJKZ771x1MDAwNVx1MDAxMFx1MDAxYmkwmT9cZjdbs+RcdTAwMTXlXHUwMDEyo1x1MDAwNHcnZ1x1MDAwNCnOyXTYO3NHXG7hyLrimVx1MDAwNjWrk+NycaBcdTAwMGIljb3hh06hWPL8Vlx1MDAwZUh/M5y/JPHxXHUwMDFmkjrIs0X67EnvNN2QIVxuXHUwMDAzk2NmfkNGV7dXXHUwMDBmqkej0f760+q4feXcV/o3ece7Jlx1MDAxYSnJXCJTXHUwMDE1/GidYEhcdTAwMWFFl5tNQ1x1MDAxNEWcRDJmpmbzRiOJk3RcdTAwMWGuxJJMljzF5mZcdTAwMDdcdTAwMDF4alx1MDAwNj2x5NcotsBs9C2PlM5cdTAwMGb3K6v1o3PSlKRcXFx1MDAxOVx1MDAxZK/nf1x1MDAwMHOwxFVkyrfvfeRcdTAwMWHx2ETc/FxmYOg8Yc3un35cYqexLVx1MDAxMVxuUEVHL1x1MDAxOLOUUT6/TdU6Wb2t3btcdTAwMWJq8NBsbFZcdTAwMGZ2Lj6vurlcdTAwMWa8XHUwMDAyaFXSXHUwMDA0XHUwMDEwodHSuZZAYCGbKKebZVFcdTAwMDExY1x1MDAwNlx1MDAwNshcdTAwMGZlWleH9ev73tnVY8O7PV+9Xt1cdTAwMWWzvYf5mNbHWd+7Xao/suKB6na2ayWzt9Pc4J/EO7XUXrhcdTAwMTT9IVxmjmbL4NKkhySpySm2sbleYFx1MDAxNuzWuC7Or1xceYWPSve1/duHp8dPPPfCg0vEaMIyXHUwMDEzQNx0VKosQ3wwO3tM0siTZlxiXHUwMDEwxjlcdTAwMDc+XHUwMDE50oU/kfw47GLtXpc+7T71qnjM9y9LzjZ+3/KD/Vx1MDAxMPnBspVcdTAwMWapYSytUsP3UlIqXHJdIIo1e1TlVIJcdTAwMThM7JpnUklsuF3ebJqEXHUwMDE4MFx1MDAwMOWSc9wwkFx1MDAxMKaMXHKZgFx1MDAxOFx1MDAwMWGSkKjJXHUwMDE1XHUwMDEyxIik3Fx1MDAxOU40kFx1MDAxMrmcJc9yXHUwMDFlr5/NeFx1MDAwYlPz16nWQlo3mVx1MDAwMFNFm9C87iBw9drGsbeeK2I1W4VcdTAwMTam42hcdTAwMDAvzbRifqyMJMXRKJLG0Hc/n76YPr7tXHUwMDExXHUwMDFh2cE3fVxi/85Sqlx1MDAxOVx1MDAxOFx1MDAwMlx1MDAwNNNcdTAwMDVykmbrtJxKNW1cZjJK2/EjsFx0L0j2nJNkkFx1MDAxNmK564NgO6ufXGJcIowkws5iSWBHKmb5TZKQlNU9XHUwMDFhL2WdupxcdTAwMGK1ucVcYkhcdTAwMTFccuKBMSGZXVlOxuPeINOMmmOBkGXOaVlyKDxlmNkjXHUwMDE4YFx1MDAwYoqWVHeNSnfXME5cdTAwMTSRdIHomHOpS71Wb3d1rb6626lueXdrjsmfaOFIXHUwMDExwKI2XHUwMDFhMzC4XHUwMDAySPprxnJQU0qBXHUwMDE2s7NawFx1MDAxMJrmT0wgaFx1MDAxOC25xtOl2S/loVx1MDAxMVxmXHUwMDAyI5R+doVcdTAwMDaPmuXOXHUwMDAx3se1UnTp7pz8XHUwMDE4Nq+p+m9r2MSfmoVhkzo3nKdGtWAkM6Ag84dcdTAwMDTGe+Kg1Nta331cdTAwMTjtuY/q02OleXyXP5RGYthcdTAwMDRQO+2Qf17DWVwiXHUwMDFljStnrvnjyGPYoCjfePGHUJAoXCJcdTAwMTNcdTAwMDDmVtH/bFNJp65cdTAwMGW6dkFcdTAwMWSbOlxynKSu60BgRGub6Tu/W/NS1lbdKubVW1x1MDAxOJ6PJXfzYeM8/zFcdTAwMTFQZlwi5tSkmINFuOSYXGJGsVx1MDAxNJdAfzJ/zcHEXHUwMDE5PNLG+HKaP0uNVIssjf6nwXGsr+1cdTAwMTHu5Yxos56xJC9cdTAwMDZcdTAwMTNVXHUwMDBivcAk2rOj4lx0K45cdTAwMWW6x1x1MDAxY5da/P7q/nZ1LX+QnkmbXHUwMDE1SE0smNKKMj93dFx1MDAxYelgvnOOXHUwMDA1XHUwMDE2Rk+X5mN+LcVAsu0qR3/Nr33n82tTfWjhXFzuWGhRMkHo/Dp4dlg5N4CNXHUwMDA3XHUwMDA2sNFcdTAwMTRTu5wwp9NLs9jFXHUwMDE1oFx1MDAwMNssfFx1MDAwM1x1MDAxNFxiL1x1MDAxMaJIa8kwmCwgKlx1MDAxOFx1MDAxOKxcdIvZU2kzVrldyoEprEVoIZlXni0xsFxuQ3Kpn5fOs787fmA99iDziMaUSYONoCrubDNIgySlhMMlmnLxvieZpI87e8RH3IJcXGFmUlx1MDAxZmEsfa5cdCVUYUHmXHUwMDBmTFZHN/XO01x1MDAwNr9xxdPp6c3tVbex5+Rd/lx1MDAwMJumSPnTNDWIXHUwMDFmQyNLfDNccqU4OGSkZlx1MDAxOa72Zn1cdEpiTuxsbpq0mVx1MDAwNpdcdTAwMTS9ZNDyyLY0r5TBQCFcdTAwMTc8g7yHzCf4i61LU71t8WFp6H56MJePtzdOeKZZTF9OSmanQ1xc1Edyjbcxboyre7vDg7XH1Y3sXHUwMDEy4pVioaVfvzM/Mc1cdTAwMThcdTAwMGavclx1MDAxY1tiw0pcdTAwMDcpXHUwMDE2cKVd3TXad/11cbZ/IdRx975Byoe5z641RqLIeoqvueGxKVx1MDAxYZnvp6HshMvpvN5cdOigXpHN2F5cdTAwMTfTsHMlgJzndVx1MDAwMdks5rL+bLZ4Qk/bo/jayVx1MDAwYmrXVMe4Ts2Wt3NFpZRcdTAwMGJcdTAwMTjiw7vdz8dPtftcdTAwMTN8+qm/XaUn643D/Cf8XHUwMDE4m1x1MDAxMk9cdTAwMTNcdTAwMDCtrcWOl7rgPKj06Vx1MDAwN4Q85Fx1MDAwNJloXHUwMDBl/Vx1MDAwYqCNXHUwMDE0QjOZhbWdOZ41MZnMTf/Z8Fx1MDAxY+1pe4T7OCM8k/RAl7SrMlx1MDAxM7OAnX7DdptcdTAwMTf79fL2idzxXHUwMDFlXHUwMDBld0Szq1x1MDAxZvOOZ1x1MDAwMpBFXHSRLm5QZO+ZrO3yXHUwMDA0XHUwMDFhLOxiP0nrW2HGuZJU5dX8/lx1MDAwYsLxq0n46knXLlxi3FSX+IxMXHUwMDEyjVxysYJ1geWO5Ua1iXeOis75ye7FRWPv9Oowh/vUzXSJXHUwMDAzRlxiXHUwMDEymMpYapqvnW12prCrLkV15I+fXHUwMDE0RKXEilx1MDAxOPLDveHfhOI//eyar3iiVPTsK061tkuwqPn9UJ9cdTAwMWLNi3ZjXVxm73S7fGxuW5dkaytcdTAwMDWlXHUwMDExtE1jlEbOL9lcdTAwMGJcdTAwMDVQ5cooooQh014oXHSlhCtcdTAwMDaYju70XHUwMDE2gSVx7b9vhyXFXG5cZqGIXHUwMDFkXHUwMDFlKF6NrI8siTzbrVx1MDAwMLnEIa/5T+F4elU+XHUwMDE5SoRv0mPhRVx1MDAxOaJcdTAwMWKY2cXosFlcdTAwMDAgZ+PS3ubNVmXteNQ831x1MDAxONyMy61rlXOAXHUwMDEwzJFd5Fx1MDAxMqCQXHUwMDA0XHUwMDEwLVx1MDAxMFx1MDAxNoqb163xllx1MDAwNlx1MDAxMMJcdTAwMThcdTAwMTJg3FxuJkgySFx1MDAxMmipb1x1MDAwNvNQnX96xdXqVIZNt49A61S92tuqr7RnL3OKKCGpm2oozFxy2Kjzs0zydFOsb5Hmo3s3qntcdTAwMDfn9VKtdJh3eFx1MDAwMp2jxkjMk/SXYlx1MDAxYVHGaHz5j8zhyVx1MDAxNVwizGhJ8fOi/Fx0iVx1MDAxNlx02ZFcdTAwMDKwoYBcdTAwMTT/eVx1MDAwMDrodJpcdTAwMDWnV1x1MDAxYvp1+73dXHUwMDFk3ja9flx1MDAxZFxmyd/bXHUwMDFkfyGsQlx1MDAxYl72jZfgWrxWc4Faflx1MDAwZjNccvn3k3YmsJtnzu/LVYNtvu+M1lx1MDAxY+fKPT6t1NeOt1x1MDAxZtJW6spcdTAwMGK2XHUwMDE5h3a1e5pQzWlcdTAwMDI3JYjbnWpcZjc0n9zU7oKMiVIqXHUwMDAzXHUwMDA1nDk5XW708m3I6azpOkpSXHUwMDEwyniBXHJcdTAwMDI+7/Ruy+O9nf3NU3p1xMa7vDvOO0Q0QFx1MDAwNNqbKiOMUmY6z1BqiowhWC/dfFx1MDAwM4mErDwyTFx1MDAxOe1vaTVcdTAwMGY/9ZdcdTAwMTVWJFx1MDAwYtvtW9WfgMZcdTAwMGKnry5b/Vnl8EPIaeKDl8pMeerGtVxmWKlNMpyfmnbX7i/cYbXbqH1cdTAwMTaDXHUwMDEyq4m1k+OTvGPTTsZcdTAwMDH0XHUwMDExbGRcdTAwMDI15Vx1MDAxOFx1MDAwMTG17bBsbGp/4rvGwjxvgp2AzVBXTKbOSTt9XHUwMDFkh8z7n56bljstYHpuoef2O8Ne2Vx1MDAwNVwi6ILq61x1MDAxNaBLoGI1761p6UJcdTAwMTWaXHUwMDBizJzNXHUwMDA0c2q+MEnfvJHYXHUwMDFkXHRcdTAwMTTnXHUwMDBiJFxuzXaM5Vx1MDAxM85EYSB6Qlx1MDAxYc1cdTAwMTPgLKVNojN2sY6vrFx1MDAxNP29cDZcdTAwMWNcdTAwMTmuid3vgPhccp9ASVxyXCLRzKVJ7pA0dl/lpbhLvytQKTBcdTAwMTE0RNeyn3g/2z9fmMpcdTAwMDa2O0ooyoWdXG5cdTAwMDGcJr7JM5hcdTAwMDRS2d1uk1fwmCs9eXbi6nSFOFx1MDAwNZ5iV1x1MDAxM6HKpnrjhL2wOaJ28Skqn5fboO87P1lcYqQj29LZo0jky7qBX/uCVKD4X1x1MDAxM2Ak+J5cdTAwMGbh34uLyFx1MDAxOVtcdFLBmSR4kX0xZ5pn+Vx1MDAxNJFcXGBcdTAwMDScQdrtJpVcdTAwMTbTUyqktFx1MDAxYolLobjdXHUwMDE2nZH0jZK+V0JcdTAwMDLfsbNIgTswuzxKotFcdTAwMGXwxYlcdTAwMTOWXHSVnEtOQus85EtCXHUwMDA2Jl72XHUwMDEycraXKCSQQEBCZ0ttp8hIjpOWWzJcYkNH+35ZQFx1MDAxZsFxd0W2Mlx1MDAxMui0YFApu2KfkFx1MDAwMqu4zCZcZkGVXHT8T/1cdTAwMTGYsGrKe5KQxe9cdTAwMTaRxVSo+KVcdTAwMDFKXHUwMDE2lJGpNiHWqeFEilx0YWCMz++w2bxrjU5OiXc/uFx1MDAxZVx1MDAxZbXcx9Od8sZFiojMUT5cdTAwMWJTSFx1MDAxOC6JXHUwMDA2ecloaMO457w2XHLQ4nGPYtb7gmOJpDCKmpf9gZOEZNwq5NLuXFzAMpCN3+ywwURcdPFN072/ySbs9jpgd/VcdTAwMGKvuSmFP35v21x1MDAwYprOrdss/D4pb3ZcdTAwMWV+X3kuev7ptcF0+/X582DYbbqFkdP8Z8tcdTAwMWQ4//pY6DqD+j+rIGucf4XveVx1MDAwZTV85SZv6lx1MDAxNpA07ddcdTAwMWKcflx1MDAwM0G1kT1X+O03v1Fcbv/733RB+OZ+ued1X59Xcas2XHUwMDA00i/8XHUwMDE23OD//e9fXHUwMDBi//jHy20r/j//c+uxWFx1MDAxZLbLXHUwMDAzwHDh7/6FRa/wd/+lXG7Fjv3khW+CR355W+v5r65bStfN52d4dTR8eFE+K063ezJcdTAwMDAoT3Q9yFx1MDAwZa/ygsegXHUwMDFmV0ae+7BcdTAwMWGXZn+r+oeNQvhax4p31ydZXz58+T8k19NTIn0= - InputsMODULE_1SUBWORKFLOW_1OutputsMODULE_4MODULE_2MODULE_3WORKFLOWSUBWORKFLOW_1MODULE_2modules.configtool argumentspublishingoutput namesbase.configcompute resourceserror strategiesprocess MODULE_2 { label "process low" input: tuple val(meta), path(fasta) output: tuple val(meta), path(fai) when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ my-function $args -i $fasta -o $fai """ } \ No newline at end of file + InputsMODULE_1SUBWORKFLOW_1OutputsMODULE_4MODULE_2MODULE_3WORKFLOWSUBWORKFLOW_1MODULE_2modules.configtool argumentspublishingoutput namesbase.configcompute resourceserror strategiesprocess MODULE_2 { label "process low" input: tuple val(meta), path(fasta) output: tuple val(meta), path(fai) when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ my-function $args -i $fasta -o $fai """ } \ No newline at end of file