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NBI-Slurm-0.19.1
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/ NBI::Launcher::RemovePrimers

NAME

NBI::Launcher::RemovePrimers

VERSION

version 0.19.1

SYNOPSIS

# Dry-run (default): print generated script
nbilaunch remove-primers \
    --r1 sample_R1.fq.gz --r2 sample_R2.fq.gz \
    --fwd-primer GTGYCAGCMGCCGCGGTAA \
    --rev-primer GGACTACNVGGGTWTCTAAT \
    --outdir results/trimmed

# Submit to Slurm
nbilaunch remove-primers ... --run

DESCRIPTION

Packaged demo launcher that trims primers from paired-end FASTQ files using cutadapt in linked-adapter mode (fwd...rev_rc on R1, rev...fwd_rc on R2). Reads without a detectable primer are discarded (--discard-untrimmed).

Primer reverse complements are computed in Perl at submission time - no seqfu or other runtime dependency needed. IUPAC degenerate bases are fully supported.

To customise this launcher for your project, copy the file to ./launchers/remove-primers.pm or ~/.nbi/launchers/remove-primers.pm and edit freely. The package declaration must remain NBI::Launcher::RemovePrimers regardless of the file's location.

NAME

NBI::Launcher::RemovePrimers - Primer removal from paired-end reads using cutadapt

METHODS

new()

Construct the RemovePrimers launcher spec. No arguments - all configuration is embedded in the constructor body (activation image, Slurm defaults, inputs, params, outputs). Returns a blessed NBI::Launcher::RemovePrimers object ready for build().

make_command(%args)

Returns the cutadapt shell invocation string for embedding in the job script. Reverse complements of both primers are computed here (IUPAC-aware) so that the exact command is visible in the saved script.

Key %args consumed here:

  • r1, r2 - absolute paths to input FASTQ files

  • fwd_primer, rev_primer - primer sequences (IUPAC bases supported)

  • threads - injected from --cpus via slurm_sync

  • sample - derived sample name (used for output filenames)

Output files reference $SCRATCH (a shell variable set by the generated script) rather than an absolute path.

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