refactor: Add gffs to ppanggolin/panaroo input

Signed-off-by: jvfe <[email protected]>
beiko-lab · May 9, 2024 · f1c93b6 · f1c93b6
1 parent b14ca29
commit f1c93b6
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/modules/local/ppanggolin/workflow/main.nf b/modules/local/ppanggolin/workflow/main.nf
@@ -11,6 +11,7 @@ process PPANGGOLIN_WORKFLOW {
 
     input:
     tuple val(meta), path(samplesheet)
+    path gffs
 
     output:
     tuple val(meta), path("$prefix")             , emit: results

diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf
@@ -9,6 +9,7 @@ process PANAROO_RUN {
 
     input:
     tuple val(meta), path(gff)
+    path gffs
 
     output:
     tuple val(meta), path("results/*")                                      , emit: results

diff --git a/subworkflows/local/phylo.nf b/subworkflows/local/phylo.nf
@@ -26,7 +26,7 @@ workflow PHYLOGENOMICS{
         ch_software_versions = Channel.empty()
 
         gffs
-            .map { meta, path -> [meta.id, path.toString()] }
+            .map { meta, path -> [meta.id, path.getName()] }
             .set { gff_paths }
 
         // Create samplesheet
@@ -39,7 +39,7 @@ workflow PHYLOGENOMICS{
                 .map{ path -> [[id: 'ppanggolin'], path] }
                 .set { gff_samplesheet }
 
-            PPANGGOLIN_WORKFLOW(gff_samplesheet)
+            PPANGGOLIN_WORKFLOW(gff_samplesheet, gffs.collect{ it[1] })
 
             PPANGGOLIN_WORKFLOW.out.pangenome.set { pangenome }
 
@@ -76,7 +76,7 @@ workflow PHYLOGENOMICS{
             * Core gene identification and alignment
             */
             // By default, run panaroo
-            PANAROO_RUN(gff_samplesheet)
+            PANAROO_RUN(gff_samplesheet, gffs.collect{ it[1] })
             PANAROO_RUN.out.aln.collect{ meta, aln -> aln }.set{ ch_core_alignment }
             PANAROO_RUN.out.accessory_aln.set{ ch_all_alignments }
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ process PPANGGOLIN_WORKFLOW { @@
         input:
         tuple val(meta), path(samplesheet)
+        path gffs
         output:
         tuple val(meta), path("$prefix")             , emit: results
@@ Expand Down @@