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The viralrecon results directory

quick look at the viralrecon results directory after the run
Now that the pipeline has completed successfully, we can have a look at the results directory

If you recall, we saved the output to results/viralrecon. Let’s change to that directory and list the files and directories:

cd results/viralrecon

There will be five directories containing results from the various steps in the viralrecon pipeline:

Directory Description
fastp Contains summary outputs for trimming and filtering reads with fastp
fastqc FastQC outputs for raw and trimmed reads
multiqc Contains the MultiQC html report which summarises outputs from the different tools used by the pipeline. This directory also contains the summary_variants_metrics_mqc.csv file we’re going to use in Week 3
pipeline_info Contains the various Nextflow outputs such as resource usage and execution times for each job
variants Contains outputs from the mapping and variant calling software bowtie2 and ivar. We’re going to use some of the vcf files produced by ivar in Week3

You’ll see that there are many different files produced by each tool. However, not all the files produced by each tool are saved in the results directory. The files that are kept are generally those that contain useful information such as the outputs from fastp and fastqc or else files that can be used further in downstream analyses. It is possible to save additional files by creating a specific configuration file that can be used when you run the pipeline but that’s beyond the scope of this course. This flexibility is another benefit of using a WfMS like Nextflow to run your analyses: nearly every parameter and output can be tweaked to produce the results you would like to see.

The main output we’re going to focus on is the MultiQC html report which we’ll go through in the next section.

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