Added min contig length param for quast into pipeline

wslh-bio · Jan 30, 2025 · 23d018c · 23d018c
1 parent d8eb070
commit 23d018c
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -61,7 +61,8 @@ Spriggan's main parameters and their defaults are shown in the table below:
 | kraken_db | Path to Kraken database for classification |
 | plus | Use AMRFinderPlus' --plus option (default: false) |
 | selected_genes | Genes of interest to pull from AMRFinderPlus output (default: 'NDM\|OXA\|KPC\|IMP\|VIM') |
-|ncbi_assembly_stats| Path to NCBI database (default: NCBI_Assembly_stats_20240124.txt)
+| ncbi_assembly_stats | Path to NCBI database (default: NCBI_Assembly_stats_20240124.txt)
+| min_quast_contig | Lower threshold for contig lenght in bp (default: 500) |
 
 ### Workflow outline
 

diff --git a/modules/local/quast.nf b/modules/local/quast.nf
@@ -6,9 +6,10 @@ process QUAST {
 
     input:
     tuple val(meta), path(contigs)
+    val(min_quast_contig)
 
     output:
-    path("${meta.id}.transposed.quast.report.tsv")                  , emit: transposed_report
+    tuple val(meta), path("${meta.id}.transposed.quast.report.tsv") , emit: transposed_report
     tuple val(meta), path("${meta.id}.quast.report.tsv")            , emit: result
     path "versions.yml"                                             , emit: versions
 
@@ -19,7 +20,7 @@ process QUAST {
     def args = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    quast.py ${contigs} -o .
+    quast.py ${contigs} -m ${min_quast_contig} -o .
     mv report.tsv ${prefix}.quast.report.tsv
     mv transposed_report.tsv ${prefix}.transposed.quast.report.tsv
 

diff --git a/nextflow.config b/nextflow.config
@@ -15,6 +15,9 @@ params {
     // QC Options
     mincoverage                = 40
 
+    // Quast
+    min_quast_contig           = 500
+
     // Trimming Parameters
     minlength                  = 10
     trimdirection              = "lr"