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Copy file name to clipboardExpand all lines: docs/session_1/1.2_run.md
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@@ -174,8 +174,6 @@ Alternatively, you could build your own execution command with the command line
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{width=100%}
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We will use `nf-core pipelines download` to download a workflow later on today.
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## 1.2.4 Executing a workflow
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Nextflow seamlessly integrates with code repositories such as [GitHub](https://github.com/). This feature allows you to manage your project code and use public Nextflow workflows — including nf-core workflows — quickly, consistently, and transparently.
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As you can see, there are a few different ways you can go about running a nextflow or nf-core pipeline. We recommend using either the `nextflow clone` command or directly cloning the repository with `git clone`. This is because it is the most flexible approach and gives you control over exacly what version of the workflow is being downloaded and where it is being downloaded to (instead of all pipelines going to `$HOME/.nextflow/assets` as with `nextflow pull`/`nextflow run`).
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The one exception to this is when you need to execute an **nf-core pipeline** in an environment **without an internet connection**. In this case, the recommendation is to use the `nf-core pipelines download` method [mentioned above](#nf-core-pipelines-download), as this tool allows you to localise all of the required configuration files and singularity images for offline use.
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## 1.2.5 Nextflow log
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It is important to keep a record of the commands you have run to generate your results. Nextflow helps with this by creating and storing metadata and logs about the run in hidden files and folders in your current directory (unless otherwise specified). This data can be used by Nextflow to generate reports. It can also be queried using the Nextflow `log` command:
Copy file name to clipboardExpand all lines: docs/session_1/1.4_rnaseq.md
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### Download the pipeline code
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!!! example "Exercise 1.4.1"
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Recall from [Lesson 1.2.3](./1.2_run.md#123-nf-core-tools) that the `nf-core` tools utility has a `download` command that can be used to localise an entire workflow along with its dependencies to your computer.
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Use the `nf-core pipelines download` command to download a local copy of the `nf-core/rnaseq` workflow that:
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As mentioned above, we will be working with version 3.23.0 of the nf-core/rnaseq pipeline for the rest of the workshop. Go ahead and download that to your working directory now.
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- Downloads pipeline version 3.23.0
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- Outputs the code base to `~/session2/nf-core-rnaseq-3.23.0/`
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- Disables downloading the prerequisite Singularity containers (since we have already prepared these beforehand for you!)
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- Downloads the institutional configs from [nf-core/configs](https://github.com/nf-core/configs)
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!!! example "Exercise 1.4.1"
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**Remember,** you can use `nf-core pipelines download --help` to review the available parameters for the `download` command.
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Clone the `nf-core/rnaseq` pipeline to your working directory. **Ensure that you download the version `3.23.0`**.
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??? success "Solution"
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We can fetch the workflow code base with the following command:
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Recall from [earlier today](1.2_run.md#124-executing-a-workflow) that we can clone a workflow with `nextflow clone`. Recall also that we can pull a specific version of the workflow with the `-r` parameter:
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```bash
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nf-core pipelines download rnaseq \
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--revision 3.23.0 \
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--outdir ~/session2/nf-core-rnaseq-3.23.0 \
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--container-system none \
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--compress none \
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--download-configuration yes
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nextflow clone -r 3.23.0 nf-core/rnaseq
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```
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The pipeline files and institutional configuration files from [nf-core/configs](https://github.com/nf-core/configs) will be downloaded to `~/session2/nf-core-rnaseq-3.23.0`. Inside this directory you will see 2 subdirectories.
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Let's have a look at the directory structure.
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The pipeline files will be downloaded to `~/session2/rnaseq`. Let's have a look at the directory structure.
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!!! example "List the downloaded directory contents"
The public [institutional configs](https://github.com/nf-core/configs) were downloaded to the `configs` directory. The code base for our pipeline will be stored in the `3_23_0` directory, named after the revision of the pipeline that we requested (`--revision 3.23.0`). The files and directories we will be working with in this session are:
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The files and directories we will be interacting with in this workshop are:
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Recall that we can print out pipeline information, including available paramters, with the `--help` parameter. Print out the available parameters for the `nf-core/rnaseq` pipeline by running:
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```bash
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nextflow run nf-core-rnaseq-3.23.0/3_23_0 --help
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nextflow run rnaseq --help
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```
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The typical or recommended run command for this pipeline is provided at the top of the screen:
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!!! example "Find the available parameters for specifying reference files"
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```bash
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nextflow run nf-core-rnaseq-3.23.0/3_23_0 --help
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nextflow run rnaseq --help
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```
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The <u>**Reference genome options**</u> section lists all of the reference file options we could possibly provide:
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Start by writing out the basic `nextflow run` command:
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```bash
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nextflow run nf-core-rnaseq-3.23.0/3_23_0 \
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nextflow run rnaseq \
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```
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**Note** that we have added a space and a backslash (` \`) to the end of the line so we may continue writing the full command over multiple lines for legibility. If you hit `Enter` now, the command won't run yet, but you will be provided a new line to continue writing.
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Next, add the `--input` parameter and pass it the path to the samplesheet. Be sure to replace `<USERNAME>` with your provided user name:
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```bash hl_lines="2"
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nextflow run nf-core-rnaseq-3.23.0/3_23_0 \
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nextflow run rnaseq \
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--input /home/<USERNAME>/data/samplesheet.csv \
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```
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Finally, add the `--outdir` parameter and give it the name `lesson-1.4`:
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```bash hl_lines="3"
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nextflow run nf-core-rnaseq-3.23.0/3_23_0 \
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nextflow run rnaseq \
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--input /home/<USERNAME>/data/samplesheet.csv \
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--outdir lesson-1.4 \
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```
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Following on from the last line from Exercise 1.4.2.1, add the `--fasta`, `--gtf`, `--star_index`, and `--salmon_index` parameters, and pass them the files we determined above in [Reference data](#reference-data):
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