modularised creation of sample file to report in a separate block

DavideBag · Nov 13, 2024 · 9687dd3 · 9687dd3
1 parent 2de9129
commit 9687dd3
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 11 deletions.
diff --git a/modules/local/report/main.nf b/modules/local/report/main.nf
@@ -12,7 +12,7 @@ process REPORT {
     path(clustersummaries)
     path(cdr3histograms)
     path(cdr3tables)
-    val (metadata)
+    path(reportsamples)
 
     output:
     path '*.RData', emit: rdata
@@ -24,13 +24,6 @@ process REPORT {
 
     script:
     def args = task.ext.args ?: ''
-    def sampleData = new File("${workDir}/sampledata.tsv")
-    sampleData.append('ID\tindividual\timmunisation\tboost\n')
-
-    // Popola il file sampledata.tsv con i dati dalla mappa metadata
-    metadata.each() { map ->
-        sampleData.append("${map.sampleID}\t${map.individualID}\t${map.immunisation}\t${map.boost}\n")
-    }
 
     // Concatena le liste dei file in stringhe separate da virgola
     clusterList = clustersummaries.join(',')
@@ -41,13 +34,12 @@ process REPORT {
 
     """
     ln -s '$moduleDir/nibsc_report.css' .
-    ln -s '${workDir}/sampledata.tsv' .
 
     quarto render analysis_report.qmd \\
         -P clusterList:\"$clusterList\" \\
         -P histoList:\"$histoList\" \\
         -P tableList:\"$tableList\" \\
-        -P sampleData:\"sampledata.tsv\" \\
+        -P sampleData:\"$reportsamples\" \\
         -P sizeThreshold:\"${params.cluster_size_threshold}\" \\
         -P loopFile:\"loop_tree.qmd" \\
         -P calcTree:\"${params.calculate_tree}\" \\

diff --git a/workflows/nanorepertoire.nf b/workflows/nanorepertoire.nf
@@ -11,6 +11,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nanorepertoire_pipeline'
 include { FASTQ_TO_FASTA         } from '../subworkflows/local/fastq_to_fasta'
 include { FASTA_CLUSTERING       } from '../subworkflows/local/fasta_clustering'
+include { REPORTSAMPLES          } from '../modules/local/reportsamples'
 include { REPORT                 } from '../modules/local/report'
 
 /*
@@ -47,13 +48,17 @@ workflow NANOREPERTOIRE {
         FASTQ_TO_FASTA.out.translated
     )
 
+    REPORTSAMPLES(
+        FASTA_CLUSTERING.out.cdrmeta.collect()
+    )
+
     REPORT(
         file("${projectDir}/assets/analysis_report.qmd"),
         file("${projectDir}/assets/loop_tree.qmd"),
         FASTA_CLUSTERING.out.clusteread.collect(),
         FASTA_CLUSTERING.out.cdrhistograms.collect(),
         FASTA_CLUSTERING.out.cdrtsv.collect(),
-        FASTA_CLUSTERING.out.cdrmeta.collect()
+        REPORTSAMPLES.out.reportsamples
     )
 
     //