Optional-phred-scores

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module
 - [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 - [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/326), allow `auto-detect` as value
+- [[#342]](https://github.com/nf-core/smrnaseq/pull/342) - Fix [phred offset issue](https://github.com/nf-core/smrnaseq/issues/341), allow specifying phred offsets for files
 
 ### Software dependencies
 

nextflow.config

@@ -68,6 +68,9 @@ params {
     pirna                       = null
     other_contamination         = null
 
+    //FASTQ handling defaults, for mirtrace
+    phred_offset = '33'
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'

nextflow_schema.json

@@ -272,6 +272,11 @@
                     "type": "boolean",
                     "description": "Save merged reads.",
                     "default": true
+                },
+                "phred_offset": {
+                    "type": "integer",
+                    "default": 33,
+                    "description": "The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format."
                 }
             }
         },

subworkflows/local/mirtrace.nf

@@ -15,7 +15,7 @@ workflow MIRTRACE {
     ch_mirtrace_config =
     reads.map { adapter, ids, reads -> [ids,reads]}
     .transpose()
-    .collectFile { id, path -> "./${path.getFileName().toString()}\n" } // operations need a channel, so, should be outside the module
+    .collectFile { id, path -> "./${path.getFileName().toString()},${params.phred_offset}\n" } // operations need a channel, so, should be outside the module
 
     MIRTRACE_RUN (
         reads,