Proof of container's concept: Get a simple version of the bash command programs to work

[cansavvy]

Issue Description

I think a good strategy here is to start out with a simple example and then we can add the wrapper and handling later. Because first we just need to know that these commands generally work on the Docker container.

What I would advise is writing just a simple bash script that carries out each of these steps for the tutorial fastq files that are found here (don't worry about the R and python scripts those will need reworking and that will be separate) https://github.com/FredHutch/pgMAP_pipeline/tree/main/input/tutorial_fastqs

Then once a basic version of this is working for the tutorial we can make a version that is wrapped and allows for multiple samples to be run and for parameters to be tweaked.

More details about the exact commands can be found here: https://github.com/FredHutch/pgMAP_pipeline/blob/main/workflow/Snakefile

I put a rough idea (copy and paste) of the command here:

• seqtk this is working as of Rearranging Dockerfile -- adding seqtk package #1
• idemp demultiplexing `{params.idemp} -b {params.ref} -n {params.n_mismatch}
  -I1 {input.barcode} -R1 {input.gRNA1} -R2 {input.gRNA2} -o {params.out_dir}
• bowtie2 -q -v 1 --best --strata --all --sam -p 4 {params.idx} {input.fastq} &> {log}
• samtools:
  • samtools sort -O bam -n {params.unsorted_bam_dir}/{params.unsorted_bam} -T {params.tmp} -o {output}
  • samtools flagstat {input} 2>{log} 1>{output}

Inputs

https://github.com/FredHutch/pgMAP_pipeline/tree/main/input/tutorial_fastqs

Your environment

The image that can be built by the Dockerfile that exists in this repo

Steps to reproduce

1. Build docker container
2. Write a simple bash script for the commands above.
3. Docker exec -it <CONTAINER_ID> bash <SCRIPT_NAME.sh>
4. Does the script complete successfully?

Pipeline behavior and error messages

Please include relevant screenshots or codeblocks with any relevant error messages. If your code ran up to a certain point before encountering an error, please include this information as well.