More descriptive names for modules and subworkflows

nf-core · Dec 6, 2024 · c69d846 · c69d846
1 parent b84b762
commit c69d846
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Showing 6 changed files with 19 additions and 21 deletions.
diff --git a/bin/plot_markers1.R b/bin/plot_markers1.R
@@ -1,5 +1,7 @@
 #!/usr/bin/env Rscript
 
+# Modified from https://gitlab.com/ezlab/busco_protocol/-/blob/main/support_protocol2/plot_markers/scripts/plot_markers1.R?ref_type=heads
+
 # load libraries
 require(RIdeogram)
 

diff --git a/modules/local/plot_busco_ideogram.nf → ...local/genome_annotation_busco_ideogram.nf b/modules/local/plot_busco_ideogram.nf → ...local/genome_annotation_busco_ideogram.nf
@@ -1,4 +1,4 @@
-process PLOT_BUSCO_IDEOGRAM {
+process GENOME_ANNOTATION_BUSCO_IDEOGRAM {
     tag "${genusspeci}_${lineage}"
     label 'process_single'
 

diff --git a/modules/local/genome_ideogram.nf → modules/local/genome_only_busco_ideogram.nf b/modules/local/genome_ideogram.nf → modules/local/genome_only_busco_ideogram.nf
@@ -1,4 +1,4 @@
-process GENOME_BUSCO_IDEOGRAM {
+process GENOME_ONLY_BUSCO_IDEOGRAM {
     tag "$meta.id"
     label 'process_single'
 
@@ -19,22 +19,18 @@ 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
     $projectDir/bin/plot_markers1.R ${prefix}_for_karyotype.txt ${prefix}
 
     # Call script for plotting
-    $projectDir/bin/plot_busco_ideogram.R --busco_output ${prefix}_busco_coordinates.txt --karyotype ${prefix}_karyotype.txt --prefix ${prefix}
+    $projectDir/bin/plot_busco_ideogram.R \\
+        --busco_output ${prefix}_busco_coordinates.txt \\
+        --karyotype ${prefix}_karyotype.txt \\
+        --prefix ${prefix} \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/subworkflows/local/genome_and_annotation.nf b/subworkflows/local/genome_and_annotation.nf
@@ -4,7 +4,7 @@ include { LONGEST                             } from '../../modules/local/longes
 include { BUSCO_BUSCO                         } from '../../modules/nf-core/busco/busco/main'
 include { QUAST                               } from '../../modules/nf-core/quast/main'
 include { AGAT_SPSTATISTICS                   } from '../../modules/nf-core/agat/spstatistics/main'
-include { PLOT_BUSCO_IDEOGRAM                 } from '../../modules/local/plot_busco_ideogram'
+include { GENOME_ANNOTATION_BUSCO_IDEOGRAM    } from '../../modules/local/genome_annotation_busco_ideogram'
 include { GFFREAD                             } from '../../modules/nf-core/gffread/main'
 include { ORTHOFINDER                         } from '../../modules/nf-core/orthofinder/main'
 include { FASTAVALIDATOR                      } from '../../modules/nf-core/fastavalidator/main'
@@ -182,7 +182,7 @@ workflow GENOME_AND_ANNOTATION {
                             }
                         }
 
-    PLOT_BUSCO_IDEOGRAM ( ch_plot_input )//removed this temporarily:, ch_karyotype
+    GENOME_ANNOTATION_BUSCO_IDEOGRAM ( ch_plot_input )//removed this temporarily:, ch_karyotype
 
     ch_tree_data        = ch_tree_data.mix(BUSCO_BUSCO.out.batch_summary.collect { meta, file -> file })
 

diff --git a/subworkflows/local/genome.nf → subworkflows/local/genome_only.nf b/subworkflows/local/genome.nf → subworkflows/local/genome_only.nf
@@ -1,9 +1,9 @@
 
 include { QUAST                               } from '../../modules/nf-core/quast/main'
 include { BUSCO_BUSCO                         } from '../../modules/nf-core/busco/busco/main'
-include { GENOME_BUSCO_IDEOGRAM               } from '../../modules/local/genome_ideogram'
+include { GENOME_ONLY_BUSCO_IDEOGRAM          } from '../../modules/local/genome_only_busco_ideogram'
 
-workflow GENOME {
+workflow GENOME_ONLY {
 
     take:
     ch_fasta // channel: [ val(meta), [ fasta ] ]
@@ -34,7 +34,7 @@ workflow GENOME {
                   | combine(ch_full_table, by:0)
 
 
-    GENOME_BUSCO_IDEOGRAM (
+    GENOME_ONLY_BUSCO_IDEOGRAM (
         ch_input_ideo
     )
 

diff --git a/workflows/genomeqc.nf b/workflows/genomeqc.nf
@@ -10,7 +10,7 @@ include { CREATE_PATH                         } from '../modules/local/create_pa
 include { NCBIGENOMEDOWNLOAD                  } from '../modules/nf-core/ncbigenomedownload/main'
 include { PIGZ_UNCOMPRESS as UNCOMPRESS_FASTA } from '../modules/nf-core/pigz/uncompress/main'
 include { PIGZ_UNCOMPRESS as UNCOMPRESS_GFF   } from '../modules/nf-core/pigz/uncompress/main'
-include { GENOME                              } from '../subworkflows/local/genome'
+include { GENOME_ONLY                         } from '../subworkflows/local/genome_only'
 include { GENOME_AND_ANNOTATION               } from '../subworkflows/local/genome_and_annotation'
 include { MULTIQC                             } from '../modules/nf-core/multiqc/main'
 include { TREE_SUMMARY                        } from '../modules/local/tree_summary'
@@ -201,13 +201,13 @@ workflow GENOMEQC {
 
     // Run genome only or genome + gff
     if (params.genome_only) {
-        GENOME (
+        GENOME_ONLY (
             ch_input.fasta
         )
         ch_multiqc_files = ch_multiqc_files
-                         | mix(GENOME.out.quast_results.map { meta, results -> results })
-                         | mix(GENOME.out.busco_short_summaries.map { meta, txt -> txt })
-        ch_versions      = ch_versions.mix(GENOME.out.versions.first())
+                         | mix(GENOME_ONLY.out.quast_results.map { meta, results -> results })
+                         | mix(GENOME_ONLY.out.busco_short_summaries.map { meta, txt -> txt })
+        ch_versions      = ch_versions.mix(GENOME_ONLY.out.versions.first())
     } else {
         GENOME_AND_ANNOTATION (
             ch_input.fasta,