test

Test subworkflow

There are tests available for Grandeur using the 'test' profile.

nextflow run UPHL-BioNGS/Grandeur -profile singularity,test

There is a caveat that this test subworkflow will not work for all users and systems because reads are downloaded using wget from the ENA. All this subworkflow does is download fastq files, so if that fails the entire subworkflow and workflow fails.

---
test subworkflow
---
flowchart LR
B["SRA Accessions"] --> fastqs
fastqs --> A["other subworkflows"]

Loading

If the test profiles do not work, the SRA accession can be downloaded from the SRA/ENA, compressed, and then used as normal files. The SRA accessions used in testing are below.

Relevant params with their default values:

params.sra_accessions      = []

# test0 and test1
params.sra_accessions      = ["SRR11725329", "SRR13643280", "SRR14436834", "SRR14634837", "SRR7738178", "SRR7889058"]
# test2-5
params.sra_accessions      = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]