From 9c74274e8d91f1b493dcaec248ecc2ac82f65f31 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toniher@cau.cat>
Date: Mon, 21 Oct 2024 21:42:09 +0200
Subject: [PATCH] moving on

---
 modules/local/exorthist/plot/get_exons.nf | 3 ++-
 modules/local/exorthist/plot/plot.nf      | 1 -
 nextflow_schema.json                      | 3 ++-
 workflows/plot.nf                         | 3 ++-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/modules/local/exorthist/plot/get_exons.nf b/modules/local/exorthist/plot/get_exons.nf
index a39a966..d026b20 100644
--- a/modules/local/exorthist/plot/get_exons.nf
+++ b/modules/local/exorthist/plot/get_exons.nf
@@ -1,11 +1,12 @@
 process GET_ISOFORM_EXONS {
     tag "${isoformID}"
     label 'pandas'
-    publishDir "${params.output}/${params.geneID}/processed_table", mode: 'copy'
+    publishDir "${params.output}/${geneID}/processed_table", mode: 'copy'
 
     input:
     val(isoformID)
     tuple val(species), path(exons_info), path(overlap_info)
+    val(geneID)
 
     output:
     stdout emit: isoform_interesting_exs
diff --git a/modules/local/exorthist/plot/plot.nf b/modules/local/exorthist/plot/plot.nf
index 013a3b9..8ca1799 100644
--- a/modules/local/exorthist/plot/plot.nf
+++ b/modules/local/exorthist/plot/plot.nf
@@ -3,7 +3,6 @@ process PLOT_EXINT {
     label 'rscript'
     // containerOptions '-B $PWD:/tmp' # TODO: To consider if this should be moved to nextflow.config
     publishDir "${params.output_plot}", mode: 'copy'
-    //publishDir "${params.output}/${params.geneID}", mode: 'copy'
 
     input:
     val(my_geneID)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index dcfbaad..49bd2d0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -91,7 +91,8 @@
         },
         "prevaln": {
           "type": "string",
-          "description": "Pre-computed alignments"
+          "description": "Pre-computed alignments",
+          "format": "directory-path"
         },
         "alignmentnum": {
           "type": "integer",
diff --git a/workflows/plot.nf b/workflows/plot.nf
index 3278574..c80a3a9 100644
--- a/workflows/plot.nf
+++ b/workflows/plot.nf
@@ -126,7 +126,8 @@ workflow PLOT {
         GENERATE_FAKE_COORDS_TABLE.out.ExNum_number_in_isoform
             .join(SUBSET_INPUT_FILES.out.overlap_info_4_isoforms)
             .join(ISOLATE_QUERY_SPECIES.out.query_species),
-        )
+        geneID
+      )
     } else {
       isoform_interesting_exs = Channel.from("None")
     }