# nfcore/rnaseq: version ${version}

## Run Name: $runName

<% if (!success){ out << """

#### nfcore/rnaseq execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: `$exitStatus`.

The full error message was:

    ${errorReport}

""" } else if(skipped_poor_alignment.size() > 0) { out << """

#### nfcore/rnaseq execution completed with warnings!

The pipeline finished successfully, but the following samples were skipped due to very low alignment (< 5%):

- `${skipped_poor_alignment.join('`
- `')}`

""" } else { out << """
nfcore/rnaseq execution completed successfully!
""" } %>

The workflow was completed at $dateComplete (duration: $duration)

The command used to launch the workflow was as follows:

    $commandLine

### Pipeline Configuration:

<% out << summary.collect{ k,v -> "
$k |
    $v
" }.join("\n") %>

nfcore/rnaseq is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

For more information, please see the pipeline homepage: https://github.com/nf-core/rnaseq