Tutorials
For teaching purposes, two paired end metagenomic sequence files are downloaded as 'Test Samples' upon the completion of the start.nf script. They are stored in the params.readDir directory, and area available for tutorial purposes.
TEST_SAMPLE_SRR11551385_1.fastq.gz- File 1TEST_SAMPLE_SRR11551385_2.fastq.gz- File 2
Tutorial: start.nf
Problem 1
Produce a command that executes the start.nf script with default parameters.
Solution
$ nextflow run start.nf
Problem 2
Produce a command that executes start.nf, downloads the SRS6485642 data from the
NCBI SRA, and stores them in a subdirectory named testReads.
Solution
$ nextflow run start.nf --SRA_IDs 'SRS6485642' --readsDir '$baseDir/testReads'
Problem 3
Produce a command that executes start.nf, renames each reference (ARG & 16S rRNA)
file to tutorial_ARG_ref.fasta and tutorial_16S_ref.fasta, respectively.
Solution
$ nextflow run start.nf --ARG_db 'tutorial_ARG_ref.fasta' --rRNA16S_db 'tutorial_16S_ref.fasta'
Tutorial: main.nf
Problem 1
Produce a command that executes the main.nf script with default parameters.
Solution
$ nextflow run main.nf
Problem 2
Produce a command that executes main.nf, and processes the aforementioned test samples.
i.e. TEST_SAMPLE_SRR11551385_1.fastq.gz & TEST_SAMPLE_SRR11551385_2.fastq.gz
Solution
$ nextflow run main.nf --reads '$baseDir/data/reads/TEST_SAMPLE_SRR11551385_{1,2}.fastq.gz'
Problem 3
Produce a command that executes main.nf, processes the test samples in Problem 2,
and changes the location that the resulting abundances will be stored to a
subdirectory called testResults in the default params.outdir directory.
Solution
$ nextflow run main.nf --reads '$baseDir/data/reads/TEST_SAMPLE_SRR11551385_{1,2}.fastq.gz' --outdir '$baseDir/results/testResults'