Integrate nf-test into parabricks-genomics

[georgiesamaha]

Integrated unit testing with https://www.nf-test.com/

[fredjaya]

0. Initialise nf-test

• Install nf-test if required
• initialise nf-test in repo

1. Develop test cases

Test cases to include. Omitting gadi-specific flags here for brevity.

1. Assert minimal command works on a samplesheet with a single .fq pair

nextflow run main.nf --input test/fq_pair_1.csv --ref test/test_chr21.fa 

2. Assert minimal command works on a samplesheet with two .fq pairs

nextflow run main.nf --input test/fq_pair_2.csv --ref test/test_chr21.fa 

3. Assert CSV samplesheets are supported

nextflow run main.nf --input test/fq_pair_1.csv --ref test/test_chr21.fa 

4. Assert TSV samplesheets are supported (to confirm - if not, assert this fails)

nextflow run main.nf --input test/fq_pair_1.tsv --ref test/test_chr21.fa 

5. Assert variant annotation with vep cache works

nextflow run main.nf --input test/fq_pair_1.csv --ref test/test_chr21.fa --download_vep_cache --vep_species homo_sapiens --vep_assembly GRCh38

6. Assert bwa_index_ch works as expected with both indexed and unindexed reference fasta files present. Index files stored in branch /test-fj

process tests

• FASTQC works on multipair single samples
• FASTQC works on singlepair single samples
• PB_FQ2BAM works on multipair single samples
• PB_FQ2BAM works on singlepair single samples

[fredjaya]

Blocked: pipeline testing with an input samplesheet cannot propagate relative paths (e.g. FASTQs). File staging deprecated in nf-test