NAME
NBI::Launcher - Base class for nbilaunch tool wrappers
VERSION
version 0.19.1
SYNOPSIS
package NBI::Launcher::MyTool;
use parent 'NBI::Launcher';
sub new {
my ($class) = @_;
return $class->SUPER::new(
name => 'mytool',
description => 'Does something useful',
version => '1.0.0',
activate => { module => 'mytool/1.0.0' },
slurm_defaults => { queue => 'short', threads => 4, memory => 8 },
inputs => [ { name => 'input', flag => '-i', type => 'file', required => 1,
help => 'Input file' } ],
params => [],
outputs => [ { name => 'result', pattern => '{sample}.out', required => 1,
help => 'Result file' } ],
outdir => { flag => '--outdir', short => '-o', required => 1 },
);
}
sub make_command {
my ($self, %args) = @_;
my $prefix = $self->singularity_prefix; # '' unless singularity activation
return "${prefix}mytool -i $args{input} -o \$SCRATCH/$args{sample}.out";
}
1;NAME
NBI::Launcher - Base class for nbilaunch tool wrappers
METHODS
new(%args)
Construct a launcher spec. See module source for all accepted keys.
activation_lines()
Shell snippet to load the tool (module load / source activate / empty for singularity).
singularity_prefix()
Returns "singularity exec $image " or "" - use in make_command() overrides.
sample_name(%args)
Derives sample name from the first required file input, stripping FASTQ extensions.
input_mode(%args)
Returns "paired" if both r1 and r2 are present, "single" otherwise.
arg_spec()
Returns the launcher's CLI surface (inputs, params, outputs, slurm_defaults). Used by nbilaunch for --help generation and argument parsing.
validate(%args)
Dies with a helpful message on missing or invalid inputs/params.
make_command(%args)
Returns the tool invocation string. Subclasses must override this. Use \$SCRATCH (literal shell variable) for scratch-directory paths.
generate_script(%args)
Assembles the full bash script body. Called by build().
build(%args)
Validates, resolves, and returns ($job, $manifest) - an NBI::Job and an NBI::Manifest - ready for nbilaunch to write and optionally submit.
AUTHOR
Andrea Telatin <proch@cpan.org>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2023-2025 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License