From 6c376c5224e555e4932012c0f56133e66d9f8445 Mon Sep 17 00:00:00 2001 From: Anne Bertolini Date: Thu, 11 Jan 2024 15:24:07 +0100 Subject: [PATCH] [FEAT] Change dsb_normalize_adt to use singularity not conda - script `dsb_normalize_adt.R`, from rule `dsb_normalize_adt` uses dsb package that is not available in conda - use custom singularity image for this step, instead of conda env --- workflow/rules/adt_dsb_normalization.smk | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/workflow/rules/adt_dsb_normalization.smk b/workflow/rules/adt_dsb_normalization.smk index ac567b4..17dd240 100644 --- a/workflow/rules/adt_dsb_normalization.smk +++ b/workflow/rules/adt_dsb_normalization.smk @@ -11,15 +11,14 @@ rule dsb_normalize_adt: CellrangerADT="results/cellranger_adt/{sample}.matrix.mtx", output: normalized="results/dsb_normalize_adt/{sample}.dsb_normalize_adt.RDS", - conda: - "../envs/dsb_normalize_adt.yaml" + singularity: + config["tools"]["dsb_normalize_adt"]["singularity"] params: adt_raw_dir=WORKDIR + "/results/cellranger_adt/{sample}/outs/raw_feature_bc_matrix/", adt_filtered_dir=WORKDIR + "/results/cellranger_adt/{sample}/outs/filtered_feature_bc_matrix/", outdir="results/dsb_normalize_adt/", - custom_script=workflow.source_path("../scripts/dsb_normalize_adt.R"), threads: config["computingResources"]["threads"]["high"] log: "logs/dsb_normalize_adt/{sample}.log", @@ -29,7 +28,7 @@ rule dsb_normalize_adt: benchmark: "results/dsb_normalize_adt/benchmark/{sample}.benchmark" shell: - "Rscript {params.custom_script} " + "Rscript workflow/scripts/dsb_normalize_adt.R " "--adt_raw_dir {params.adt_raw_dir} " "--adt_filtered_dir {params.adt_filtered_dir} " "--outdir {params.outdir} "