moving on

biocorecrg · Oct 21, 2024 · 9c74274 · 9c74274
1 parent 166ea27
commit 9c74274
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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")
     }