| Table of Contents |
|---|
| minLevel | 1 |
|---|
| maxLevel | 6 |
|---|
| outline | false |
|---|
| style | none |
|---|
| type | list |
|---|
| printable | true |
|---|
|
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.
| Code Block |
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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:
...
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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:
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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:
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nextflow log agitated_bose |
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/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
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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:
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nextflow log agitated_bose -t template.html > nextflow_run_report.html |