/ 
SimpleFlow-0.13
/ README.md

A tiny workflow manager and logger for Perl, like SnakeMake or NextFlow, but in pure Perl and aimed at making long, error-prone shell pipelines easy to debug and reproduce.

Every step is a single task() call. SimpleFlow checks the inputs before a command runs and the outputs after, times the command, captures its stdout, stderr, exit code and signal, optionally logs a full structured record, and skips work that has already been done.

Two subroutines are exported by default: task and say2.

Install

With a CPAN client:

cpanm SimpleFlow

Or from a checkout:

perl Makefile.PL
make
make test
make install

Synopsis

The simplest useful case: run a command and confirm it produced its output:

use SimpleFlow qw(task say2);

my $t = task({
    cmd            => 'which ls',
    'output.files' => '/tmp/AFK3mnEK8L.log',
});

task returns a hash reference describing exactly what happened:

{
    cmd            "which ls",
    die            1,
    dir            "/home/con/Scripts/SimpleFlow",
    done           "now",
    dry.run        0,
    duration       0.00191903114318848,
    exit           0,
    note           "",
    output.files   [
        [0] "/tmp/AFK3mnEK8L.log"
    ],
    overwrite      1,
    signal         0,
    source.file    "t/01.t",
    source.line    29,
    stderr         "",
    stdout         "/usr/bin/ls",
    will.do        "done"
}

Portability note. SimpleFlow runs whatever shell command you give it via system(), so the commands themselves are your responsibility to keep cross-platform (e.g. which ls is Unix-only). SimpleFlow's own behaviour exit/signal decoding and coloured output is cross-platform; see the change log.

task

my $result = task(\%args);

Runs one shell command with checking, timing, capture and logging. Takes a single hash reference; the only required key is cmd.

Arguments

| Key | Type | Default | Description | |----------------|------------------|---------|-------------| | cmd | scalar | undef | Required. The shell command to run. | | die | bool (0/1) | 1 | Die if the command fails (non-zero exit) or an output file is missing. Set to 0 to warn and continue instead. | | dry.run | bool | 0 | Print the command (and log it) but do not execute it. | | input.files | scalar or array | undef | File(s) that must exist and be readable before running; otherwise task dies. | | output.files | scalar or array | undef | File(s) expected to exist after running; used both for the missing-output check and for skip detection. | | log.fh | open filehandle | undef | If given, the full result record is also written here. Must be a real, open filehandle. | | note | scalar | '' | Free-text note copied into the result and the log. | | overwrite | bool | 0 | If false and all output.files already exist, the command is skipped. Set true to always run. |

Passing an unrecognised key, an empty filename, or a non-filehandle log.fh causes task to die: these are usually mistakes worth catching early.

Return value

task always returns a hash reference. The fields below are present after a normal run; the skip and dry-run paths omit the execution-only fields (exit, signal, stdout, stderr).

| Field | Meaning | |--------------------|---------| | cmd | The command that was run. | | dir | Working directory at execution time. | | done | "now" (just ran), "before" (skipped, outputs already existed), or "not yet" (dry run). | | will.do | "done", "no" (skipped), "no: dry run", or "FAILED". | | duration | Wall-clock seconds the command took (0 for skips/dry runs). | | exit | Exit code of the command (-1 if it could not be launched). | | signal | Signal number if the command process was killed by a signal, else 0. Always 0 on Windows (no POSIX signals). | | stdout, stderr | Captured output, with trailing whitespace stripped. | | die, dry.run, overwrite, note | The (defaulted) argument values used. | | output.files | Array ref of the output files (a scalar argument is normalised to a one-element array). | | output.file.size | Hash of filename => size in bytes for the outputs. | | input.files | The input argument, as given (present only if you passed input.files). | | input.file.size | Hash of filename => size in bytes for the inputs (present only if you passed input.files). | | source.file, source.line | Where in your code the task was called: handy when debugging a long pipeline. |

Skipping completed work

If overwrite is false (the default) and every file in output.files already exists, task does not re-run the command. This makes pipelines restartable: re-running the script picks up where it left off.

open my $log, '>', 'logfile.txt';
my $t = task({
    cmd            => 'gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr',
    'input.files'  => ['em.mdp', 'box.gro', 'topol.top'],
    'output.files' => 'em.tpr',
    'log.fh'       => $log,
});
close $log;

On the first run done is "now"; on a re-run (with em.tpr present) done is "before" and will.do is "no". Pass overwrite => 1 to force it.

Dry runs

Useful for inspecting a pipeline without executing anything expensive:

my $t = task({
    cmd       => 'a long-running, time-consuming command',
    'dry.run' => 1,
    'log.fh'  => $fh,
});

The command is printed (and logged) but not run; will.do is "no: dry run".

Failure behaviour

By default (die => 1) task dies if the command exits non-zero or if any declared output.files are missing afterwards, so a broken step stops the pipeline immediately. With die => 0, task instead warns and returns its result hash (with will.do => "FAILED"), letting you decide what to do.

say2

say2($message, $filehandle);

"Say to two places": prints $message to standard output and to the given log filehandle, prefixed with the calling file and line number so log entries are traceable. The filehandle must be open, or say2 dies.

open my $log, '>', 'run.log';
say2('starting equilibration', $log);   # -> STDOUT and run.log
close $log;

Dependencies

Core/runtime modules used by SimpleFlow:

The test suite additionally uses Test::More and Test::Exception.

Change log

0.13 (2026-06-11)

Fixed (Claude Opus 4.8 helped)

Changed / Windows support

Tests

0.12

exit code now matches what shell would show it as; signal now appears

0.11

max string length now corresponds to max of output strings, no more truncated output added List::Util dependency for string length maxes memory size now shows when output directory is now output during dry runs