MultiQC at OSC

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# Running MultiQC at OSC

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### Jelmer Poelstra, MCIC Wooster
### 2021/02/12 (updated: 2021-02-11)

---

## MultiQC

MultiQC is a program that *aggregates and summarizes QC log files* into a single
nicely formatted HTML page.

It is most often used to summarize FastQC results, but can also be used to
summarize STAR and featureCounts output logs, as we'll do later.

---

## MultiQC

- For instance, this figure shows mean quality scores across 132 samples:

---

## MultiQC and Conda at OSC

MultiQC is *not* available as a module at OSC (i.e., no `module load`).

The best way to use it is by installing it for yourself
**with the software manager Conda**, which:
  
  - Creates *environments* with one (best-practice) or more software packages.

- Lots of bioinformatics software is available as a Conda package.
  
  - Handles dependencies but does not require admin rights.
  
  - Environments are activated and deactivated like with the `module` system.

---

## Conda at OSC

- To use Conda at OSC, you first need to load a module:

```sh
  $ module load python/3.6-conda5.2
  ```
  
  .content-box-info[
  Like with other software, this module needs to be loaded every time you
  want to use Conda.
  ]

---

## One-time installation of MultiQC into a Conda environment

- Now, we are ready to create a new Conda environment with Python: 
 
  ```sh
  $ conda create -y -n multiqc-env python=3.7
  ```

- `create` is the Conda command to create a new environment.
  
  - `-y` avoids a confirmation prompt.
  
  - `-n multiqc-env` is the name for the new environment, which is arbitrary.
  
  - `python=3.7` is how specify that we want to install Python and specifically,
     Python version 3.7.
  
---

## One-time installation of MultiQC into a Conda environment

- Next, we *activate* the environment and install MultiQC into it:

```sh
  $ source activate multiqc-env
  
  $ conda install -y -c bioconda -c conda-forge multiqc
  ```

- `-c bioconda -c conda-forge` is how we indicate which so-called
    *channels*, i.e. repositories, we want to use.
    (These sorts of details are provided in software installation instructions.)

---

## Running MultiQC from now on

- Now that we have MultiQC installed into a Conda environment at OSC,  
  we just need to take the following steps whenever we want to use it:
  
  ```sh
  $ module load python/3.6-conda5.2
  $ source activate multiqc-env
  ```

- Having done that, you should be able to run MultiQC:

```sh
  $ multiqc --help
  ```

.content-box-info[
If you didn't manage to create your own conda environment,  
you can also use mine:

```sh
$ source activate /users/PAS0471/jelmer/.conda/envs/multiqc
```
]

---

## Running MultiQC

Actually running MultiQC is straightforward:

```sh
# This will put the MultiQC report in the working dir:
$ multiqc <dir-with-fastqc-reports>

# You can also specify the output dir for the MultiQC report: 
$ multiqc <dir-with-fastqc-reports> -o <output-dir>
```

For example, to start an interactive job and run MultiQC there:

```sh
$ cd /fs/project/PAS0471/teach/misc/2021-02_rnaseq/$USER

# Start an interactive job at OSC:
$ sinteractive -A PAS0471 # No time specified: will be 30 minutes

$ module load python/3.6-conda5.2  # Load the conda module
$ source activate multiqc          # Activate the MultiQC env.

$ multiqc results/QC_fastq/ -o results/QC_fastq/ # Run MultiQC

$ ls -lh results/QC_fastq/multiqc_report.html    # Main output file
```

---

## MultiQC output

.content-box-diy[
Let's take a look at the output file via OnDemand's file browser.
]

---

## MultiQC script

We could also run MultiQC in a script (`scripts/QC_fastq/multiqc.sh`):

```sh
#!/bin/bash
#SBATCH --account=PAS0471
#SBATCH --time=60
#SBATCH --out=slurm-multiqc-%j.out
set -e -u -o pipefail

# Save command-line arguments in named variables:
input_dir="$1"
output_dir="$2"

mkdir -p "$output_dir" # If necessary, create the output dir

# Report before starting the pogram:
echo "Running MultiQC for dir: $input_dir"
echo "Output dir: $output_dir"

# Load the conda module and the MultiQC conda environment:
module load python/3.6-conda5.2
source activate /users/PAS0471/jelmer/.conda/envs/multiqc

# Run fastqc:
multiqc "$input_dir" -o "$output_dir"
```

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## Running our MultiQC script

- Submitting the script as a job:
  ```sh
  $ dir=results/QC_fastq/
  $ sbatch multiqc.sh $dir $dir
  ```

- Checking the queue:
  ```sh
  $ squeue -u $USER
  ```

- Checking the output:
  ```sh
  $ ls
  
  $ less slurm*
  
  $ ls $dir/multiqc_report.html
  ```

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# Questions?

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