feat: add psltools

modules/nextflow/psltools/convert/main.nf

@@ -0,0 +1,62 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_CONVERT — Convert PSL to BED
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_CONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.bed")       , optional: true, emit: bed
+    tuple val(meta), path("*.bed.gz")    , optional: true, emit: bed_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def type      = task.ext.type ?: '12'
+    def gzip      = task.ext.gzip ? "--gzip" : ""
+    """
+    psltools convert \\
+        $args \\
+        $gzip \\
+        --psl $psl \\
+        --out ${prefix}.bed \\
+        --type $type
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed
+    touch ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/psltools/filter/main.nf

@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_FILTER — Filter PSL files by score, strand, or other criteria.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_FILTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools filter \\
+        $args \\
+        --psl $psl \\
+        --out-psl ${prefix}.filtered.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/psltools/merge/main.nf

@@ -0,0 +1,60 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_MERGE — Merge PSL files into a single PSL file.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_MERGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psls)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    ls *.psl > psl.list
+
+    psltools merge \\
+        $args \\
+        --file psl.list \\
+        --out-psl ${prefix}.merged.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.merged.psl
+    touch ${prefix}.merged.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/psltools/score/main.nf

@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SCORE — Score PSL files by summing the values of the alignment scores.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SCORE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.tsv")       , optional: true, emit: tsv
+    tuple val(meta), path("*.tsv.gz")    , optional: true, emit: tsv_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools score \\
+        $args \\
+        --psl $psl \\
+        --out ${prefix}.scores.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+    touch ${prefix}.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/psltools/sort/main.nf

@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SORT — Sort PSL files by chromosome, start, or other criteria.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools sort \\
+        $args \\
+        --psl $psl \\
+        --out ${prefix}.scores.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}

modules/nextflow/psltools/split/main.nf

@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SPLIT — Split PSL files into multiple PSL files.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SPLIT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools split \\
+        $args \\
+        --psl $psl \\
+        --out-prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}