Removed redundant lines and updated modules.config

nf-core · Dec 9, 2024 · fe07df8 · fe07df8
1 parent c69d846
commit fe07df8
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Showing 3 changed files with 8 additions and 10 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -151,15 +151,15 @@ process {
         ]
     }
 
-    withName: 'PLOT_BUSCO_IDEOGRAM' {
+    withName: 'GENOME_ANNOTATION_BUSCO_IDEOGRAM' {
         publishDir = [
-            path: { "${params.outdir}/busco_ideogram" },
+            path: { "${params.outdir}/genome_annotation_busco_ideogram" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: 'GENOME_BUSCO_IDEOGRAM' {
+    withName: 'GENOME_ONLY_BUSCO_IDEOGRAM' {
         publishDir = [
             path: { "${params.outdir}/genome_busco_ideogram" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/genome_only_busco_ideogram.nf b/modules/local/genome_only_busco_ideogram.nf
@@ -21,12 +21,12 @@ process GENOME_ONLY_BUSCO_IDEOGRAM {
 
     # Get chromosome lengths:
     seqkit fx2tab -i -n -l ${genome} > ${prefix}_for_karyotype.txt
-    
+
     # Call script for table wrangling
-    $projectDir/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
+    plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
 
     # Call script for plotting
-    $projectDir/bin/plot_busco_ideogram.R \\
+    plot_busco_ideogram.R \\
         --busco_output ${prefix}_busco_coordinates.txt \\
         --karyotype ${prefix}_karyotype.txt \\
         --prefix ${prefix} \\

diff --git a/subworkflows/local/genome_and_annotation.nf b/subworkflows/local/genome_and_annotation.nf
@@ -52,7 +52,7 @@ workflow GENOME_AND_ANNOTATION {
                  | combine(ch_gff_agat, by:0) // by:0 | Only combine when both channels share the same id
                  | combine(ch_gff_long, by:0)
                  | multiMap {
-                     meta, fasta, gff_unfilt, gff_filt ->
+                     meta, fasta, gff_unfilt, gff_filt -> // null is is probably not necessary
                          fasta      : fasta      ? tuple( meta, file(fasta)      ) : null // channel: [ val(meta), [ fasta ] ]
                          gff_unfilt : gff_unfilt ? tuple( meta, file(gff_unfilt) ) : null // channel: [ val(meta), [ gff ] ], unfiltered
                          gff_filt   : gff_filt   ? tuple( meta, file(gff_filt)   ) : null // channel: [ val(meta), [ gff ] ], filtered for longest isoform
@@ -134,8 +134,6 @@ workflow GENOME_AND_ANNOTATION {
     // MODULE: Run BUSCO
     //
 
-    //GFFREAD.out.gffread_fasta.collect().view()
-
     BUSCO_BUSCO (
         GFFREAD.out.gffread_fasta,
         "proteins", // hardcoded
@@ -182,7 +180,7 @@ workflow GENOME_AND_ANNOTATION {
                             }
                         }
 
-    GENOME_ANNOTATION_BUSCO_IDEOGRAM ( ch_plot_input )//removed this temporarily:, ch_karyotype
+    GENOME_ANNOTATION_BUSCO_IDEOGRAM ( ch_plot_input )
 
     ch_tree_data        = ch_tree_data.mix(BUSCO_BUSCO.out.batch_summary.collect { meta, file -> file })