From 9fcb3eec0300e70f7dd476251ae09f7d3b1f7028 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Fri, 12 Apr 2024 11:10:19 -0400 Subject: [PATCH] fix: use container for cutadapt --- config/config.yaml | 1 + workflow/rules/preprocessing.smk | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index ec3ed0d..d91d1b0 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -119,6 +119,7 @@ containers: bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0" circexplorer: 'docker://nciccbr/ccbr_circexplorer:v1.0' clear: "docker://nciccbr/ccbr_clear:latest" + cutadapt: 'nciccbr/ncigb_cutadapt_v1.18:latest' dcc: "docker://nciccbr/charlie_dcc:v0.1.0" mapsplice: "docker://cgrlab/mapsplice2:latest" nclscan: "docker://nciccbr/charlie_nclscan:v0.1.0" diff --git a/workflow/rules/preprocessing.smk b/workflow/rules/preprocessing.smk index daf2f99..61d463a 100644 --- a/workflow/rules/preprocessing.smk +++ b/workflow/rules/preprocessing.smk @@ -31,8 +31,7 @@ rule cutadapt: cutadapt_q=config["cutadapt_q"], adapters=join(RESOURCES_DIR, "TruSeq_and_nextera_adapters.consolidated.fa"), randomstr=str(uuid.uuid4()), - envmodules: - TOOLS["cutadapt"]["version"], + container: config['containers']['cutadapt'] threads: getthreads("cutadapt") shell: """