Workflow caching and checkpointing

Last updated on 2024-12-04 | Edit this page

Overview

Questions

  • How can I restart a Nextflow workflow after an error?
  • How can I add new data to a workflow without starting from the beginning?
  • Where can I find intermediate data and results?

Objectives

  • Resume a Nextflow workflow using the -resume option.
  • Restart a Nextflow workflow using new data.

A key feature of workflow management systems, like Nextflow, is re-entrancy, which is the ability to restart a pipeline after an error from the last successfully executed process. Re-entrancy enables time consuming successfully completed steps, such as index creation, to be skipped when adding more data to a pipeline. This in turn leads to faster prototyping and development of workflows, and faster analyses of additional data. Nextflow achieves re-entrancy by automatically keeping track of all the processes executed in your pipeline via caching and checkpointing.

Resume

To restart from the last successfully executed process we add the command line option -resume to the Nextflow command.

For example, the command below would resume the word_count.nf script from the last successful process.

BASH 

$ nextflow run word_count.nf --input 'data/yeast/reads/ref1*.fq.gz' -resume

We can see in the output that the results from the process NUM_LINES has been retrieved from the cache.

OUTPUT 

Launching `word_count.nf` [condescending_dalembert] - revision: fede04a544
[c9/2597d5] process > NUM_LINES (1) [100%] 2 of 2, cached: 2 ✔
ref1_1.fq.gz 58708

ref1_2.fq.gz 58708

Resume a pipeline

Resume the Nextflow script word_count.nf by re-running the command and adding the parameter -resume and the parameter --input 'data/yeast/reads/temp33*':

BASH 

$ nextflow run word_count.nf --input 'data/yeast/reads/temp33*' -resume

If your previous run was successful the output will look similar to this:

OUTPUT 

N E X T F L O W  ~  version 20.10.0
Launching `word_count.nf` [nauseous_leavitt] - revision: fede04a544
[21/6116de] process > NUM_LINES (4) [100%] 6 of 6, cached: 6 ✔
temp33_3_2.fq.gz 88956

temp33_3_1.fq.gz 88956

temp33_1_1.fq.gz 82372

temp33_2_2.fq.gz 63116

temp33_1_2.fq.gz 82372

temp33_2_1.fq.gz 63116

You will see that the execution of the process NUMLINES is actually skipped (cached text appears), and the results are retrieved from the cache.

How does resume work?

Nextflow stores all intermediate files and task results during the execution of a workflow is work directory. It acts as a scratch space where all the temporary data required for the workflow’s execution is kept. Within the work directory, Nextflow creates subdirectories named with unique hashes (e.g., work/ab/cd1234…). Each of these subdirectories corresponds to a specific process or task in the pipeline. The hashed directory names ensure that each task’s outputs are isolated and uniquely identified.

The mechanism works by assigning a unique ID to each task. This unique ID is used to create a separate execution directory, within the work directory, where the tasks are executed and the results stored. 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

When we resume a workflow Nextflow uses this unique ID to check if:

  1. The working directory exists
  2. It contains a valid command exit status
  3. It contains the expected output files.

If these conditions are satisfied, the task execution is skipped and the previously computed outputs are applied. When a task requires recomputation, ie. the conditions above are not fulfilled, the downstream tasks are automatically invalidated.

Therefore, if you modify some parts of your script, or alter the input data using -resume, will only execute the processes that are actually changed.

The execution of the processes that are not changed will be skipped and the cached result used instead.

This helps a lot when testing or modifying part of your pipeline without having to re-execute it from scratch.

Modify Nextflow script and re-run.

Alter the timestamp on the file temp33_3_2.fq.gz using the UNIX touch command.

BASH 

$ touch data/yeast/reads/temp33_3_2.fq.gz

Run command below.

BASH 

$ nextflow run word_count.nf --input 'data/yeast/reads/temp33*' -resume

How many processes will be cached and how many will run ?

The output will look similar to this:

OUTPUT 

N E X T F L O W  ~  version 20.10.0
Launching `word_count.nf` [gigantic_minsky] - revision: fede04a544
executor >  local (1)
[20/cda0d5] process > NUM_LINES (5) [100%] 6 of 6, cached: 5 ✔
temp33_1_2.fq.gz 82372

temp33_3_1.fq.gz 88956

temp33_2_1.fq.gz 63116

temp33_1_1.fq.gz 82372

temp33_2_2.fq.gz 63116

temp33_3_2.fq.gz 88956

As you changed the timestamp on one file it will only re-run that process. The results for the other 5 processes are retrieved from the cache.

The Work directory

By default the pipeline results are cached in the directory work where the pipeline is launched.

We can use the Bash tree command to list the contents of the work directory. Note: By default tree does not print hidden files (those beginning with a dot .). Use the -a to view all files.

BASH 

$ tree -a work

Example output

OUTPUT 

work/
├── 12
│   └── 5489f3c7dbd521c0e43f43b4c1f352
│       ├── .command.begin
│       ├── .command.err
│       ├── .command.log
│       ├── .command.out
│       ├── .command.run
│       ├── .command.sh
│       ├── .exitcode
│       └── temp33_1_2.fq.gz -> /home/training/data/yeast/reads/temp33_1_2.fq.gz
├── 3b
│   └── a3fb24ad3242e4cc8e5aa0c24d174b
│       ├── .command.begin
│       ├── .command.err
│       ├── .command.log
│       ├── .command.out
│       ├── .command.run
│       ├── .command.sh
│       ├── .exitcode
│       └── temp33_2_1.fq.gz -> /home/training/data/yeast/reads/temp33_2_1.fq.gz
├── 4c
│   └── 125b5e5a5ee144fa25dd9bccd467e9
│       ├── .command.begin
│       ├── .command.err
│       ├── .command.log
│       ├── .command.out
│       ├── .command.run
│       ├── .command.sh
│       ├── .exitcode
│       └── temp33_3_1.fq.gz -> /home/training/data/yeast/reads/temp33_3_1.fq.gz
├── 54
│   └── eb9d72e9ac24af8183de569ab0b977
│       ├── .command.begin
│       ├── .command.err
│       ├── .command.log
│       ├── .command.out
│       ├── .command.run
│       ├── .command.sh
│       ├── .exitcode
│       └── temp33_2_2.fq.gz -> /home/training/data/yeast/reads/temp33_2_2.fq.gz
├── e9
│   └── 31f28c291481342cc45d4e176a200a
│       ├── .command.begin
│       ├── .command.err
│       ├── .command.log
│       ├── .command.out
│       ├── .command.run
│       ├── .command.sh
│       ├── .exitcode
│       └── temp33_1_1.fq.gz -> /home/training/data/yeast/reads/temp33_1_1.fq.gz
└── fa
    └── cd3e49b63eadd6248aa357083763c1
        ├── .command.begin
        ├── .command.err
        ├── .command.log
        ├── .command.out
        ├── .command.run
        ├── .command.sh
        ├── .exitcode
        └── temp33_3_2.fq.gz -> /home/training/data/yeast/reads/temp33_3_2.fq.gz

Task execution directory

Within the work directory there are multiple task execution directories. There is one directory for each time a process is executed. These task directories are identified by the process execution hash. For example the task directory fa/cd3e49b63eadd6248aa357083763c1 would be location for the process identified by the hash fa/cd3e49 .

The task execution directory contains:

  • .command.sh: The command script. The .command.sh file includes the specific instructions you’ve written to process your data or perform computations.

  • .command.run: A Bash script generated by Nextflow to manage the execution environment of the .command.sh script. This script acts as a wrapper around .command.sh. It performs several tasks like setting up the task’s environment variables, handling the task’s pre and post execution (like moving inputs and outputs to correct locations, logging start and end times, handling errors, and ensuring resource limits are respected

  • .command.out: The complete job standard output.

  • .command.err: The complete job standard error.

  • .command.log: The wrapper execution output.

  • .command.begin: A file created as soon as the job is launched.

  • .exitcode: A file containing the task exit code. This file is used to capture and store the exit status of the process that was run by the .command.sh script.

  • Any task input files (symlinks)

  • Any task output files

Specifying another work directory

Depending on your script, this work folder can take a lot of disk space. You can specify another work directory using the command line option -w. Note Using a different work directory will mean that any jobs will need to re-run from the beginning.

BASH 

$ nextflow run word_count.nf --input 'data/yeast/reads/temp33*' -w second_work_dir -resume

OUTPUT 

N E X T F L O W  ~  version 21.04.0
Launching `word_count.nf` [deadly_easley] - revision: fede04a544
executor >  local (6)
[9d/0f5e89] process > NUM_LINES (5) [100%] 6 of 6 ✔
temp33_3_2.fq.gz 88956

temp33_1_1.fq.gz 82372

temp33_3_1.fq.gz 88956

temp33_1_2.fq.gz 82372

temp33_2_2.fq.gz 63116

temp33_2_1.fq.gz 63116

Clean the work directory

If you are sure you won’t resume your pipeline execution, clean this folder periodically using the command nextflow clean.

BASH 

$ nextflow clean [run_name|session_id] [options]

Supply the option -n to print names of files to be removed without deleting them, or -f to force the removal of the files. If you only want to remove files from a run but retain execution log entries and metadata, add the option -k. Multiple runs can be cleaned with the options, -before, -after or -but before the run name. For example, the command below would remove all the temporary files and log entries for runs before the run gigantic_minsky.

BASH 

$ nextflow clean -f -before gigantic_minsky

Remove a Nextflow run.

Remove the last Nextflow run using the command nextflow clean. First use the option -dry-run to see which files would be deleted and then re-run removing the run and associated files.

An example nextflow clean command with dry-run .

BASH 

$ nextflow clean nauseous_leavitt -dry-run

An example nextflow clean command removing the files.

BASH 

$ nextflow clean nauseous_leavitt -f

Key Points

  • Nextflow automatically keeps track of all the processes executed in your pipeline via checkpointing.
  • Nextflow caches intermediate data in task directories within the work directory.
  • Nextflow caching and checkpointing allows re-entrancy into a workflow after a pipeline error or using new data, skipping steps that have been successfully executed.
  • Re-entrancy is enabled using the -resume option.