Reporting

Overview

Teaching: 20 min
Exercises: 5 min

Questions

• How do I get information about my pipeline run?

• How can I see what commands I ran?

• How can I create a report from my run?

Objectives

• View Nextflow pipeline run logs.

• Use nextflow log to view more information about a specific run.

• Create an HTML report from a pipeline run.

Nextflow log

Once a script has run, Nextflow stores a log of all the workflows executed in the current folder. Similar to an electronic lab book, this means you have a have a record of all processing steps and commands run.

You can print Nextflow’s execution history and log information using the nextflow log command.

$ nextflow log

TIMESTAMP          	DURATION	RUN NAME               	STATUS	REVISION ID	SESSION ID                          	COMMAND

This will print a summary of the executions log and runtime information for all pipelines run. By default, included in the summary, are the date and time it ran, how long it ran for, the run name, run status, a revision ID, the session id and the command run on the command line.

Show Execution Log

Listing the execution logs of previous invocations of all pipelines in a directory.

$ nextflow log

Solution

The output will look similar to this:

TIMESTAMP          	DURATION	RUN NAME       	STATUS	REVISION ID	SESSION ID                          	COMMAND
2021-03-19 13:45:53	6.5s    	fervent_babbage	OK    	c54a707593 	15487395-443a-4835-9198-229f6ad7a7fd	nextflow run wc.nf
2021-03-19 13:46:53	6.6s    	soggy_miescher 	OK    	c54a707593 	58da0ccf-63f9-42e4-ba4b-1c349348ece5	nextflow run wc.nf --samples 'data/yeast/reads/*.fq.gz'

Pipeline execution report

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 tiny_fermat

/data/.../work/7b/3753ff13b1fa5348d2d9b6f512153a
/data/.../work/c1/56a36d8f498c99ac6cba31e85b3e0c
/data/.../work/f7/659c65ef60582d9713252bcfbcc310
/data/.../work/82/ba67e3175bd9e6479d4310e5a92f99
/data/.../work/e5/2816b9d4e7b402bfdd6597c2c2403d
/data/.../work/3b/3485d00b0115f89e4c202eacf82eba

This will list the work directory for each process.

Task ID

A task’s unique ID is generated as a 128-bit hash number obtained from a composition of the task’s:

• Inputs values
• Input files
• Command line string
• Container ID
• Conda environment
• Environment modules
• Any executed scripts in the bin directory

Fields

If we want to print more metadata we can use log command and the option -f (fields) followed by a comma delimited list of fields. This can be composed to track the provenance of a workflow result.

For example:

$ nextflow log tiny_fermat -f 'process,exit,hash,duration'

Will output the process name, exit status, hash and duration of the process for the tiny_fermat run to the terminal.

INDEX	0	7b/3753ff	2s
FASTQC	0	c1/56a36d	9.3s
FASTQC	0	f7/659c65	9.1s
QUANT	0	82/ba67e3	2.7s
QUANT	0	e5/2816b9	3.2s
MULTIQC	0	3b/3485d0	6.3s

The complete list of available fields can be retrieved with the command:

$ nextflow log -l

attempt
complete
container
cpus
disk
duration
env
error_action
exit
hash
inv_ctxt
log
memory
module
name
native_id
pcpu
peak_rss
peak_vmem
pmem
process
queue
rchar
read_bytes
realtime
rss
scratch
script
start
status
stderr
stdout
submit
syscr
syscw
tag
task_id
time
vmem
vol_ctxt
wchar
workdir
write_bytes

Script

If we want a log of all the commands executed in the pipeline we can use the script field. It is important to note that the resultant output can not be used to run the pipeline steps.

Filtering

The output from the log command can be very long. We can subset the output using the option -F (filter) specifying the filtering criteria. This will print only those tasks matching a pattern using the syntax ~=/<pattern>/.

For example to filter for process with the name FASTQC we would run:

$ nextflow log tiny_fermat -F 'process =~ /FASTQC/'

/data/.../work/c1/56a36d8f498c99ac6cba31e85b3e0c
/data/.../work/f7/659c65ef60582d9713252bcfbcc310

This can be useful to locate specific tasks work directories.

View run log

Use the Nextflow log command specifying a run name and the fields. name, hash, process and status

Solution

$ nextflow log elegant_descartes -f name,hash,process,status

Filter pipeline run log

Use the -F option and a regular expression to filter the for a specific process.

Solution

$ nextflow log elegant_descartes -f name,hash,process,status -F 'process =~ /MULTIQC/'

Templates

The -t option allows a template (string or file) to be specified. This makes it possible to create a custom report in any text based format.

For example you could save this markdown snippet to a file:

## $name

script:

    $script

exist status: $exit
task status: $status
task folder: $folder

Then, the following log command will output a markdown file containing the script, exit status and folder of all executed tasks:

nextflow log elegant_descartes -t my-template.md > execution-report.md

Or, the template file can also be written in HTML.

For example:

<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>

By saving the above snippet in a file named template.html, you can run the following command:

$ nextflow log elegant_descartes -t template.html > provenance.html

To view the report open it in a browser.

Generate an HTML run report

Generate an HTML report for a run using the -t option and the template.html file.

Solution

$ nextflow log elegant_descartes -t template.html > provenance.html

Key Points

• Nextflow can produce a custom execution report with run information using the log command.

• You can generate a report using the -t option specifying a template file.