Test data¶

Overview¶

Four test samples are included with the pipeline. Two samples will fail tresholds (one failing pipeline thresholds, one failing the labroatory threshold) and two which will pass.

Samplesheet¶

sample,fastq_1,fastq_2 sample1,sample1.R1.fastq.gz,sample1.R2.fastq.gz sample2,sample2.R1.fastq.gz,sample2.R2.fastq.gz sample3,sample3.R1.fastq.gz,sample3.R2.fastq.gz sample4,sample4.R1.fastq.gz,sample4.R2.fastq.gz

Lab Results¶

sample,results sample,results sample1,Providencia sample2,Acinetobacter sample3,Klebsiella sample4,Pseudomonas

Expected Results¶

Sample1¶

This sample will fail QC thesholds. KRAKEN2_CLASSIFY_WEIGHTED : FAILED : Genus-Acinetobacter is under 70% (species-baumannii 66.25%), likely contaminated ASSEMBLY_RATIO(SD) : FAILED : St. dev. too large - 1.8449x(7.4691-SD) against P.stuartii COVERAGE : FAILED : 4.16x coverage based on trimmed reads (Min:30x)

Sample2¶

This sample will pass all QC thresholds.

Sample3¶

This sample will fail QC thresholds. The results should be Pseudomonas, but reported as Klebsiella

Sample4¶

This sample will pass all QC thresholdss.

Running pipeline¶

To execute with Docker:

nextflow run main.nf -entry arANALYSIS -profile docker,test

To execute with Singularity:

nextflow run main.nf -entry arANALYSIS -profile singularity,test

To execute with the provided wrapper:

bash run_workflow.sh \
  -e arANALYSIS \
  -i test

Last update: 2025-01-29