From e9abaa22377d0f50afc41c8bf7db47a78d953fc5 Mon Sep 17 00:00:00 2001 From: slsevilla Date: Sun, 31 Mar 2024 16:32:21 +0000 Subject: [PATCH] refactor: move fastp variables to config #150 --- nextflow.config | 2 ++ workflows/phoenix.nf | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 55eb08ef..a6841eb1 100755 --- 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 index 9d7357af..df8e7c93 100644 --- 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)