From 30fdd530c5d98b1b8e433f3d67d2d8e456324074 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 19 Nov 2024 16:01:58 +0100 Subject: [PATCH] fix styling --- docs/hello_nextflow/09_hello_nf-core.md | 4 ++-- .../img/pipeline.excalidraw.svg | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 docs/hello_nextflow/img/pipeline.excalidraw.svg diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 5db06747..3ca0a1e3 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -525,7 +525,7 @@ Now let's add another tool to the pipeline. In your pipeline, you will add a new step that will take FASTQ files from the sample sheet as inputs and will produce trimmed fastq files that can be used as an input for other tools and version information about the seqtk tools to mix into the inputs for the MultiQC process.
- --8<-- "docs/nf_develop/img/pipeline.excalidraw.svg" + --8<-- "docs/img/pipeline.excalidraw.svg"
The `nf-core modules install` command can be used to install the `seqtk/trim` module directly from the nf-core repository: @@ -995,7 +995,7 @@ nf-core pipelines typically use samplesheets as inputs to the pipelines. This al Samplesheets are comma-separated text files with a header row specifying the column names, followed by one entry per row. For example, the samplesheet that we have been using during this teaching module looks like this: -```console "samplesheet_test_illumina_amplicon.csv" +```console title="samplesheet_test_illumina_amplicon.csv" sample,fastq_1,fastq_2 SAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz SAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz diff --git a/docs/hello_nextflow/img/pipeline.excalidraw.svg b/docs/hello_nextflow/img/pipeline.excalidraw.svg new file mode 100644 index 00000000..ae940126 --- /dev/null +++ b/docs/hello_nextflow/img/pipeline.excalidraw.svg @@ -0,0 +1,21 @@ + + + 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 + + + + + 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