Collect Metrics suggestion

KThorellGroup · Nov 28, 2024 · a94f865 · a94f865
1 parent bb7a20d
commit a94f865
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/bactpipe.nf b/bactpipe.nf
@@ -84,12 +84,19 @@ workflow {
     SHOVILL(FASTP.out.fastq)
     ASSEMBLY_STATS(SHOVILL.out.contigs)
 
+    ch_assembly_metrics = ASSEMBLY_STATS.out.splitCsv(skip: 1)
+        .map { row -> row.join('\t') }
+    ch_mqc_metrics = Channel.value("TODO: header goes here")
+        .concat(ch_metrics)
+        .collectFile( newLine: true, sort: false )
+
     prokka_ch = (SHOVILL.out.contigs).join(CLASSIFY_TAXONOMY.out.classification)
 
     PROKKA(prokka_ch)
 
     MULTIQC(
         FASTP.out.fastp_reports.collect(),
+        ch_mqc_metrics ),
         PROKKA.out.collect()
     )
 }

diff --git a/modules/assembly_stats/assembly_stats.nf b/modules/assembly_stats/assembly_stats.nf
@@ -4,10 +4,10 @@ process ASSEMBLY_STATS {
     publishDir "${params.output_dir}/shovill", mode: 'copy'
 
     input:
-    tuple val(pair_id), file("${pair_id}.contigs.fa")
+    tuple val(pair_id), path("${pair_id}.contigs.fa")
 
     output:
-    file("${pair_id}.assembly_stats.txt")
+    path("${pair_id}.assembly_stats.txt")
 
     script:
     """

diff --git a/modules/multiqc/multiqc.nf b/modules/multiqc/multiqc.nf
@@ -4,6 +4,7 @@ process MULTIQC {
 
     input:
     path('*.json')
+    path('assembly_metrics_mqc.tsv')
     path('*_prokka')
 
     output:
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,7 @@ process MULTIQC { @@
         input:
         path('*.json')
+        path('assembly_metrics_mqc.tsv')
         path('*_prokka')
         output:
@@ Expand Down @@