Create new columns in sample_summary.tsv

[jessicarowell]

Created 3 new columns:
opxv_reads_1 -> filepath to seqtk output, reads file 1
opxv_reads_2 -> filepath to seqtk output, reads file 2
final_assembly -> filepath to final assembly

Test command:
nextflow run main.nf --indir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/paired/ --outdir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/results/ --project_name test -config /scicomp/reference/nextflow/configs/cdc-dev.config -profile singularity,rosalind

PR checklist

• [ x] This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mpxvassembly branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[mikeyweigand]

Make sure outputs are full paths to fasta and fastq, even if user input is a relative path.

[jessicarowell]

I've added a line to convert relative to absolute paths for outdir

[jessicarowell]

@mikeyweigand Right now this code only outputs a path for final_assembly if there is a <sample>.final.fa file. If there are only <sample>.draft.fa assemblies, these are ignored and the column is left blank. Is this the expected behavior or should I modify?

[jessicarowell]

Whoops. Sorry about that...blaming it on Friday. Thanks for fixing it.

[mikeyweigand]

@mikeyweigand Right now this code only outputs a path for final_assembly if there is a <sample>.final.fa file. If there are only <sample>.draft.fa assemblies, these are ignored and the column is left blank. Is this the expected behavior or should I modify?

Agree this makes the most sense, current 'ask' is to streamline capture of necessary inputs for TOSTADAS, to which you wouldn't send a draft contig fasta.

[mikeyweigand]

Looks good. Tested and performs as expected.