feat: Add verticall pairwise module

modules/local/verticall.nf

@@ -0,0 +1,52 @@
+process VERTICALL {
+    tag "$cluster"
+    label 'process_high'
+
+ conda "bioconda::verticall=0.4.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/verticall:0.4.1--pyhdfd78af_0':
+        'quay.io/biocontainers/verticall:0.4.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(cluster), path(assemblies), val(reference)
+    path assembly_files
+
+    output:
+    tuple val(cluster), path("verticall_${prefix}.tsv"), emit: tsv
+    path "versions.yml"                                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${cluster}"
+    """
+    mkdir assemblies_dir
+
+    for s in \$(cut -f2 -d"\t" $assemblies); do cp \$s assemblies_dir/; done
+
+    verticall \\
+        pairwise \\
+        $args \\
+        -i assemblies_dir/ \\
+        --threads $task.cpus \\
+        -o verticall_${prefix}.tsv \\
+        -r assemblies_dir/$reference
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        verticall: \$(echo \$(verticall --version 2>&1) | sed "s/^Verticall v//g")
+    END_VERSIONS
+    """
+    stub:
+    prefix = task.ext.prefix ?: "${cluster}"
+    """
+    touch verticall_${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        verticall: \$(echo \$(verticall --version 2>&1) | sed "s/^Verticall v//g")
+    END_VERSIONS
+    """
+}

recombination.nf

@@ -1,4 +1,5 @@
 include { GET_RECOMB_INPUT } from './modules/local/get_recomb_input'
+include { VERTICALL } from './modules/local/verticall'
 
 
 workflow {
@@ -35,7 +36,7 @@ workflow {
 
         GET_RECOMB_INPUT.out.csv
             .splitCsv(header: true)
-            .map { row -> tuple(row.Cluster, file(row.samplesheet), row.Reference, file(row.reference_path)) }
+            .map { row -> tuple(row.Cluster, file(row.samplesheet), row.Reference, row.reference_path) }
             .set { recomb_input }
 
         assemblies
@@ -45,10 +46,10 @@ workflow {
             .collect { meta, path -> path }
             .set { unduplicated_assemblies }
 
-        // SKA (
-        //     ska_input.map { c, s, r, rf -> tuple(c,s,rf) },
-        //     unduplicated_assemblies
-        //  )
+        VERTICALL (
+            recomb_input.map { c, s, r, rf -> tuple(c,s,rf) },
+            assemblies.collect { meta, path -> path }
+        )