Commit 45438142 authored by Lukas Jelonek's avatar Lukas Jelonek
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parent e02ef52d
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In this exercise you will create a workflow that runs fastqc on a set of fastq
files and aggregates the reports with multiqc. Hint: Run your workflow after
each step of the exercise.
each step of the exercise. Use the `-resume` option to avoid recomputation of
results.
### Setup
......@@ -55,7 +56,6 @@ As a task is executed in it's own task directory and the input files are staged
inside that directory (be sure to use the file qualifier!) we can use the
default fastqc behaviour and just call it with the file.
### Define output channels
Fastqc created two files: a html and a zip file. For the aggregated report with
......@@ -75,7 +75,10 @@ specific pattern. Check the documentation at
https://www.nextflow.io/docs/latest/process.html#publishdir to find out how.
By default nextflow creates symbolic links in the results directory to the
files. This can also be configured. Look it up in the documentation.
files. While this saves a lot of space it has the downside that your results
will depend on the work directory. To avoid that you can configure the
publishing behaviour. Check the documentation and let nextflow copy the
results.
(Optional) Define a tag for the execution, e.g. the file name or the file
prefix.
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