Fixed ideogram not working for genome mode

nf-core · Dec 6, 2024 · b84b762 · b84b762
1 parent a43634a
commit b84b762
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Showing 5 changed files with 24 additions and 44 deletions.
diff --git a/bin/plot_markers1.R b/bin/plot_markers1.R
@@ -19,7 +19,11 @@ colnames(karyotype1) <- c("Chr", "End", "Start", "species", "size", "color")
 # reorder columns
 karyotype <- karyotype1[, c(1,3,2,4,5,6)]
 
-write.table(karyotype, file = paste0("data/karyotype/", out_name, "_karyotype.txt"), quote = FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
+# debugging code
+print("Karyotype table\n")
+head(karyotype)
+
+write.table(karyotype, file = paste0(out_name, "_karyotype.txt"), quote = FALSE, row.names = FALSE, col.names = TRUE, sep = "\t")
 
 
 

diff --git a/bin/plot_markers2.R b/bin/plot_markers2.R
diff --git a/conf/modules.config b/conf/modules.config
@@ -159,6 +159,14 @@ process {
         ]
     }
 
+    withName: 'GENOME_BUSCO_IDEOGRAM' {
+        publishDir = [
+            path: { "${params.outdir}/genome_busco_ideogram" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'GENE_OVERLAPS' {
         publishDir = [
             path: { "${params.outdir}/gene_overlaps" },

diff --git a/modules/local/genome_ideogram.nf b/modules/local/genome_ideogram.nf
@@ -19,15 +19,22 @@ process GENOME_BUSCO_IDEOGRAM {
     """
     grep -v "#" ${busco_full_table} | cut -f 2,3,4,5  | grep -v "Missing" > ${prefix}_busco_coordinates.txt
 
+    #echo "Current directory: \$(pwd)"
+    #echo "Contents of current directory:"
+    #ls -l
+    #echo "Contents of projectDir:"
+    #ls -l $projectDir/bin
+    #echo "Contents of plot_markers1.R script"
+    #cat $projectDir/bin/plot_markers1.R
 
     # Get chromosome lengths:
     seqkit fx2tab -i -n -l ${genome} > ${prefix}_for_karyotype.txt
     
     # Call script for table wrangling
-    Rscript /home/ucbtfrd/pipelines/genomeqc/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
+    $projectDir/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
 
     # Call script for plotting
-    Rscript /home/ucbtfrd/pipelines/genomeqc/bin/plot_markers2.R ${prefix}_karyotype.txt ${prefix}_busco_coordinates.txt ${prefix}
+    $projectDir/bin/plot_busco_ideogram.R --busco_output ${prefix}_busco_coordinates.txt --karyotype ${prefix}_karyotype.txt --prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
@@ -4,8 +4,8 @@ process BUSCO_BUSCO {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
-        'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.8.0--pyhdfd78af_0':
+        'biocontainers/busco:5.8.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta, stageAs:'tmp_input/*')