From 6605810fb53b24e289ac0f29b216aecfc589aa96 Mon Sep 17 00:00:00 2001 From: Zachary Nolen Date: Sun, 16 Feb 2025 12:00:50 +0100 Subject: [PATCH] Allow params to be passed to fastp separately for merged or paired processing --- .test/config/config.yaml | 3 ++- config/config.yaml | 3 ++- workflow/rules/1.0_preprocessing.smk | 4 ++-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.test/config/config.yaml b/.test/config/config.yaml index aaf6fe6..1d8ab95 100644 --- a/.test/config/config.yaml +++ b/.test/config/config.yaml @@ -121,7 +121,8 @@ params: clipoverlap: clip_user_provided_bams: true fastp: - extra: "-p -g" # don't put --merge or --overlap_len_require here, they're implicit + merged_extra: "-p -g" # don't put --merge or --overlap_len_require here, they're implicit + paired_extra: "-p -g" min_overlap_hist: 20 bwa_aln: extra: "-l 16500 -n 0.01 -o 2" diff --git a/config/config.yaml b/config/config.yaml index c05badf..d0dd3cf 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -119,7 +119,8 @@ params: clipoverlap: clip_user_provided_bams: false fastp: - extra: "-p -g" # don't put --merge or --overlap_len_require here, they're implicit + merged_extra: "-p -g" # don't put --merge or --overlap_len_require here, they're implicit + paired_extra: "-p -g" min_overlap_hist: 30 bwa_aln: extra: "-l 16500 -n 0.01 -o 2" diff --git a/workflow/rules/1.0_preprocessing.smk b/workflow/rules/1.0_preprocessing.smk index 216b016..3fe4a71 100644 --- a/workflow/rules/1.0_preprocessing.smk +++ b/workflow/rules/1.0_preprocessing.smk @@ -50,7 +50,7 @@ rule fastp_mergedout: benchmark: "benchmarks/preprocessing/fastp/{sample}_{unit}_{lib}.merged.log" params: - extra=lambda w: config["params"]["fastp"]["extra"] + extra=lambda w: config["params"]["fastp"]["merged_extra"] + f" --merge --overlap_len_require {config['params']['fastp']['min_overlap_hist']}", threads: lambda wildcards, attempt: attempt * 2 resources: @@ -87,7 +87,7 @@ rule fastp_pairedout: benchmark: "benchmarks/preprocessing/fastp/{sample}_{unit}_{lib}.paired.log" params: - extra=lambda w: config["params"]["fastp"]["extra"], + extra=lambda w: config["params"]["fastp"]["paired_extra"], threads: lambda wildcards, attempt: attempt * 2 resources: runtime=lambda wildcards, attempt: attempt * 480,