Results folder
The results are output in the folder name specified in the .nexftlow.config file under the outdir parameter. It is generally set to be results.
params {
outdir = 'results'
}
Nextflow log, metrics and reports
By default, Nextflow will create a log file in the working directory called .nextflow.log. This file is hidden but you can see it using the command:
ls -a
If you rerun the pipeline in the same folder, the previous .nextflow.log will be renamed .nextflow.log.1 and a new .nextflow.log will be generated.
You can change the default location by specifying a different location
nextflow -log ~/code/nextflow.log run
You can list the execution logs of previous invocations of all pipelines in a directory by running the command:
nextflow log
TIMESTAMP DURATION RUN NAME STATUS REVISION ID SESSION ID COMMAND 2024-09-23 15:38:11 27m 5s cranky_pike OK 5901bea438 449030e3-e32d-4010-bc1c-9d6f1f62cc45 nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 2024-09-24 14:18:37 1m 45s agitated_bose OK 5901bea438 449030e3-e32d-4010-bc1c-9d6f1f62cc45 nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 -resume --multiqc_title smrnaseq
If we want to get more information about an individual run we can add the run name or session ID to the log command.
For example:
nextflow log agitated_bose
/mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/d5/fd4b1581fd60a640f586ca9557e425 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/20/88bac48f8031d973e7d47e215baf73 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/6d/427866552c311523327e16d3ec0b32 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/c0/aa328b61d23c7f1ca738aa5f5fc142 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/b5/3e73ab56f65b707a1db9767ce472ea /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/aa/35a63e37a55434920fc7f3e4a99c80 /mnt/hpccs01/home/gauthiem/smrnaseq_cl/work/95/6d0db42195231bb9861871c7700798 ...
Generate an html run report
cat <<EOF > my_template.html
<div>
<h2>\${name}</h2>
<div>
Script:
<pre>\${script}</pre>
</div>
<ul>
<li>Exit: \${exit}</li>
<li>Status: \${status}</li>
<li>Work dir: \${workdir}</li>
<li>Container: \${container}</li>
</ul>
</div>
EOF
Run the following command:
nextflow log agitated_bose -t template.html > nextflow_run_report.html