fix up params + usage

nf-core · Jun 19, 2024 · 4dd03ca · 4dd03ca
1 parent e45e521
commit 4dd03ca
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -78,7 +78,8 @@ params {
     skip_markduplicates        = false
     skip_alignment             = false
     skip_pseudo_alignment      = false
-    strand_predict_threshold   = 0.8
+    stranded_threshold         = 0.8
+    unstranded_threshold       = 0.1
 
     // QC
     skip_qc                    = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -453,13 +453,20 @@
                     "default": 200,
                     "fa_icon": "fas fa-sort-amount-up-alt"
                 },
-                "strand_predict_threshold": {
+                "stranded_threshold": {
                     "type": "number",
                     "minimum": 0.5,
                     "maximum": 1.0,
                     "default": 0.8,
                     "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5.",
                     "help_text": "To be assigned as unstranded, read fractions must be different by less than 1- this value. Samples not convincingly assigned as stranded or unstranded will be assigned as 'undetermined'. These will be treated as unstranded but flagged as potential problems in the final MultiQC report."
+                },
+                "unstranded_threshold": {
+                    "type": "number",
+                    "minimum": 0.0,
+                    "maximum": 1.0,
+                    "default": 0.1,
+                    "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'"
                 }
             }
         },

diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
@@ -312,7 +312,7 @@ workflow RNASEQ {
         .lib_format_counts
         .join(ch_strand_fastq.auto_strand)
         .map { meta, json, reads ->
-            def salmon_strand_analysis = getSalmonInferredStrandedness(json, threshold = params.strand_predict_threshold)
+            def salmon_strand_analysis = getSalmonInferredStrandedness(json, stranded_threshold = params.stranded_threshold, unstranded_threshold = params.unstranded_threshold)
             strandedness = salmon_strand_analysis.inferred_strandedness
             if ( strandedness == 'undetermined' ){
                 strandedness = 'unstranded'
@@ -744,7 +744,7 @@ workflow RNASEQ {
             ch_strand_comparison = BAM_RSEQC.out.inferexperiment_txt
                 .map {
                     meta, strand_log ->
-                        def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, threshold = params.strand_predict_threshold)
+                        def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, stranded_threshold = params.stranded_threshold, unstranded_threshold = params.unstranded_threshold)
                         rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness
 
                         def status = 'fail'