sangerseq nextflow pipeline

[sebschulz1]

Goal is to create a nextflow pipeline based on the bulk sangerseq prototype.
Based on previous discussions, I have created a draft scheme of a potential pipeline that still requires discussion and refinement.
Firest steps would be to create docker files and images for the pipeline steps that currently don't run in containers, i.e. pre-processing and post-processing.

[sebschulz1]

The pipeline development branch is here: https://github.com/biosustain/dsp_bulk-sangerseq/tree/nextflow

The nf-core guidelines es were followed.

Test using profile
Run succeeded!

Command used from root directory:

nextflow run . -profile docker,test

Assessment of output folders and files

• align dir: quick check reveals that all expected files are generated (detailed analysis outstanding)
• decompose: Indigo visualisations (.html) are absent.
• assemble: quick check reveals that all expected files are generated (detailed analysis outstanding)
• vuegen_report: is generated as .html file in vuegen_report/rendered_report_quarto_report
  - finalizing the VUEGEN_REPORT process appears relatively long.

Test using custom data
Run succeeded!

Command executed from bash file in root directory (example command shown):

nextflow run . -profile docker \
  --data_dir  ./path/to/data/dir \
  --samplesheet ./path/to/samplesheet.csv \
  --reference_fasta ./path/to/reference_file.fa \
  --outdir ./outdir/nf_test_run_2

Assessment of output folders and files
Same observrations as in Test using profile.

Recommendations

• Update docs with path/to/outdirectoryor similar (currently it only says results)

Test using nf-test
OUTSTANDING

Next steps

• Test runs with different parameters, in particular trimming parameters
• Detailed investigation of outfiles to ensure results integrity