Alignment workflow

[rlancaster96]

Full nextflow alignment workflow

• [x] input param of path to folder containing one patient both tumor and normal fastq files
• [ ] array for potentially intaking multiple fastq files to bwa-mem2 alignment
• [x] use channels instead of pointing to paths using params
• [x] auto-generate dirs needed for fastqc

Questions for future:

• do we want to save all files, including middle steps (such as sorting before markduplicates) or are there only certain files we want to save in the interest of space?

[rlancaster96]

• added an example for a params file needed to run align.wf
• reorganized workflows dir (because of this reorganizing, file paths no longer match up, so committing this branch to main would remove ability to run with individual workflows, you will have to use align.nf)

[rlancaster96]

note: because I overwrote the tool.nf files, merging this branch to main will break anything that relied on these tools previously (including the old draft align.nf).

[elisabethgoldman]

Full nextflow alignment workflow

• [x] input param of path to folder containing one patient both tumor and normal fastq files
• [ ] array for potentially intaking multiple fastq files to bwa-mem2 alignment
• [x] use channels instead of pointing to paths using params
• [x] auto-generate dirs needed for fastqc

Questions for future:

• do we want to save all files, including middle steps (such as sorting before markduplicates) or are there only certain files we want to save in the interest of space?

Let's get rid of the large intermediate files, like unsorted bams, since we just mark but don't toss out the duplicates info. Given we have a small data set, I would keep the intermediates until we/test user runs the workflow from end to end successfully (i.e., don't explicitly code in their removal just yet).