chore(#3): Copy over Homer modules

modules/local/homer/createuniqmap/main.nf

@@ -0,0 +1,45 @@
+process HOMER_CREATEUNIQMAP {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'process_long'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+        'biocontainers/homer:4.11--pl526hc9558a2_3' }"
+
+    input:
+    path(mappable_regions)
+
+    output:
+    path("uniqmap/"), emit: uniqmap_dir
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11'
+    """
+    mkdir -p uniqmap
+    homerTools special uniqmap uniqmap/ $mappable_regions
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def VERSION = '4.11'
+    """
+    mkdir -p uniqmap
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
+}

modules/local/homer/getmappableregions/main.nf

@@ -0,0 +1,52 @@
+process HOMER_GETMAPPABLEREGIONS {
+    tag "${fasta_files[0].baseName}"
+    label 'process_high_memory'
+    label 'process_long'
+
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+        'community.wave.seqera.io/library/homer:4.11--e7dc4a041f589d54' }"
+
+    input:
+    path(fasta_files, arity: '1..*')
+    val(parallel_sequences)
+    val(read_length)
+
+    output:
+    path("*.txt"), emit: txt
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${fasta_files[0].baseName}"
+    def VERSION = '4.11'
+    """
+    getMappableRegions \\
+        $parallel_sequences \\
+        $read_length \\
+        $fasta_files \\
+        > ${prefix}.${read_length}nt.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11'
+    """
+    touch ${prefix}.${read_length}nt.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        homer: $VERSION
+    END_VERSIONS
+    """
+}