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Fix broken img urls #31

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merged 1 commit into from Mar 22, 2024
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Fix broken img urls #31

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4 changes: 2 additions & 2 deletions docs/walkthroughs/nextflow-custom-workflows/nextflow-custom.md
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Expand Up @@ -9,11 +9,11 @@ Suggested reading before starting this tutorial:

Workflow management systems such as Nextflow can be used to create reproducible and scalable workflows. This tutorial consists of taking a test pipeline with the following workflow:

<img src="../../img/workflow1.png" alt= "Workflow1" height="400">
<img src="../../../img/workflow1.png" alt= "Workflow1" height="400">

And modifying and extending it to follow this workflow:

<img src="../../img/workflow2.png" alt= "Workflow2" height="500">
<img src="../../../img/workflow2.png" alt= "Workflow2" height="500">

## TASK 1: Try running the test pipeline

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6 changes: 4 additions & 2 deletions docs/walkthroughs/nfcore.md
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Expand Up @@ -13,7 +13,9 @@ Some examples of nf-core pipelines include:
* [nf-core/taxprofiler](https://nf-co.re/taxprofiler/): to run multiple taxonomy profiling tools on a metagenomics dataset
* [nf-core/mag](https://nf-co.re/mag/): to assemble and bin whole metagenome sequencing runs

See the full list [online](https://nf-co.re/pipelines).
* See the full list [online](https://nf-co.re/pipelines).

* 💡 See also [Using Nextflow](../../notebook-servers/using-nextflow)

## How to run a nf-core pipeline?

Expand Down Expand Up @@ -70,7 +72,7 @@ nextflow run nf-core/fetchngs -r 1.12.0 \

Example execution:

<img src="../img/nf-fetch-run.png" alt="nf-core fetchngs execution" height="500">
<img src="../../img/nf-fetch-run.png" alt="nf-core fetchngs execution" height="500">

## S3 buckets

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2 changes: 1 addition & 1 deletion docs/walkthroughs/qiime2.md
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Expand Up @@ -4,7 +4,7 @@

QIIME 2 ([Boylan et al., 2019](https://www.nature.com/articles/s41587-019-0209-9)) is a microbiome analysis package with an emphasis on data transparency. In short it allows for end-to-end analysis, including demupltiplexing, noise correction, taxonomic classification, phylogeny inference and plotting. Below is a flow chart of the conceptual outline of QIIME 2 (courtesy of the authors, found [here](https://docs.qiime2.org/2023.7/tutorials/overview/)).

<img src="../img/qiime.png" alt= "Qiime">
<img src="../../img/qiime.png" alt= "Qiime">

## Installation

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