03_assignment.qmd

---
title: "Week 3: Assignment"
format: html
---

## In-class

1. Pull the `samtools` Docker container:

```bash
module load Apptainer/1.1.6
apptainer pull docker://biocontainers/samtools:v1.9-4-deb_cv1
```

2. Open a shell in the Docker container:

```bash
apptainer shell docker://biocontainers/samtools:v1.9-4-deb_cv1
```

Try accessing files in your `/home/username/` directory:

```bash
ls -l /home/laderast/bash_for_bio/
```

That didn't work - exit the shell:

```
exit
```

3. Bind your directory so that the Docker container can see it:

```bash
apptainer shell --bind /user/tladera2/bash_for_bio:/bash_for_bio docker://biocontainers/samtools:v1.9-4-deb_cv1
```

Try accessing files in `bash_for_bio/`

```bash
samtools view -c bash_for_bio/data/MOLM13_combined_final.sam > bash_for_bio/MOLM13_counts.txt
```

```bash
exit
```

4. Try running the command using `apptainer exec`:

```bash
apptainer exec \
    --bind /users/tladera2/bash_for_bio:/bash_for_bio \ 
    docker://biocontainers/samtools:v1.9-4-deb_cv1 \ 
    samtools view -c bash_for_bio/data/MOLM13_combined_final.sam > \
    /bash_for_bio/MOLM13_combined_final.counts.txt
```

## Homework

1. Adapt the for loop in this script to use `apptainer exec`. You can use an ubuntu container for this. 

```bash
#!/bin/bash
for file in ./data/*.fastq
do
  wc $file
done
```

2. Modify `run_bwa.sh` in `week3/` to use apptainer for bwa. Hints: you will need to load Apptainer,  and use `apptainer exec`. To make things easier, pull the bwa container first. 

```bash
#!/bin/bash
module load BWA/0.7.17-GCCcore-11.2.0
input_fastq=${1}
# strip path and suffix
base_file_name="${input_fastq%.fastq}"
base_file_name=${base_file_name##*/}
echo "running $input_fastq"
sample_name="SM:${base_file_name}"
read_group_id="ID:${base_file_name}"
platform_info="PL:Illumina"
ref_fasta_local="/shared/biodata/reference/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"

bwa mem \
      -p -v 3 -M \
      -R "@RG\t${read_group_id}\t${sample_name}\t${platform_info}" \
      "${ref_fasta_local}" "${input_fastq}" > \
      "${base_file_name}.sam"

module purge
```


Run the `run_bwa.sh` script on one of the files to ensure that it works.

```bash

```

Try using `week3/run_sbatch.sh` on the files in the `data/` directory. Were there any modifications you needed to make to `run_sbatch.sh`?

```bash

```