feat: Create panaroo samplesheet (#103)

* feat: Create panaroo samplesheet * feat: Make panaroo ignore invalid annotation
beiko-lab · May 2, 2023 · 4bcd833 · 4bcd833
1 parent 3c96481
commit 4bcd833
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -326,7 +326,7 @@ process {
     //  pangenomics
 
     withName: PANAROO_RUN {
-        ext.args = "-a pan --clean-mode strict --len_dif_percent 0.70 -c 0.7 -f 0.5"
+        ext.args = "-a pan --clean-mode strict --len_dif_percent 0.70 -c 0.7 -f 0.5 --remove-invalid-genes"
         publishDir = [
             path: { "${params.outdir}/pangenomics/panaroo" },
             mode: params.publish_dir_mode,

diff --git a/subworkflows/local/phylo.nf b/subworkflows/local/phylo.nf
@@ -21,11 +21,21 @@ workflow PHYLOGENOMICS{
     main:
         ch_software_versions = Channel.empty()
 
+        // Create Panaroo samplesheet
+        gffs
+            .map { meta, path -> [meta.id, path.toString()] }
+            .collectFile(newLine: true) { item ->
+                [ "${item[0]}.txt", item[1] ]
+            }
+            .collectFile(name: 'panaroo_samplesheet.txt')
+            .map{ path -> [[id: 'panaroo'], path] }
+            .set { gff_samplesheet }
+
         /*
         * Core gene identification and alignment
         */
         // By default, run panaroo
-        PANAROO_RUN(gffs.collect{ meta, gff -> gff}.map( gff -> [[id: 'panaroo'], gff]))
+        PANAROO_RUN(gff_samplesheet)
         PANAROO_RUN.out.aln.collect{meta, aln -> aln }.set{ ch_core_gene_alignment }
         PANAROO_RUN.out.graph_gml.map{ id, path -> path }.set { panaroo_graph }
         ch_software_versions = ch_software_versions.mix(PANAROO_RUN.out.versions.ifEmpty(null))