refactor: move fastp variables to config CDCgov#150

slsevilla · Mar 31, 2024 · e9abaa2 · e9abaa2
1 parent f33a04a
commit e9abaa2
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -27,6 +27,8 @@ params {
     // Params for filtering
     minlength                   = 500
     phred                       = 33
+    save_trimmed_fail           = true
+    save_merged                 = false
 
     // Additional input parameters for -entry SRA and CDC_SRA
     input_sra                   = null

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -153,7 +153,7 @@ workflow PHOENIX_EXTERNAL {
 
         // Trim and remove low quality reads
         FASTP_TRIMD (
-            BBDUK.out.reads, true, false
+            BBDUK.out.reads, params.save_trimmed_fail, params.save_merged
         )
         ch_versions = ch_versions.mix(FASTP_TRIMD.out.versions)