From 76ec524580501465cec18f76cdd8f881c6ef9f6a Mon Sep 17 00:00:00 2001 From: Gali Bai Date: Fri, 23 Jul 2021 10:42:56 -0400 Subject: [PATCH] fix path when feeding multi parameters to --STARsolo Features --- MAESTRO/Snakemake/scRNA/rules/sc_rna_map.smk | 6 +++--- MAESTRO/Snakemake/scRNA/rules/sc_rna_merge.smk | 6 +++--- MAESTRO/Snakemake/scRNA/rules/sc_rna_qc.smk | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/MAESTRO/Snakemake/scRNA/rules/sc_rna_map.smk b/MAESTRO/Snakemake/scRNA/rules/sc_rna_map.smk index 66da54e..72b2f7c 100644 --- a/MAESTRO/Snakemake/scRNA/rules/sc_rna_map.smk +++ b/MAESTRO/Snakemake/scRNA/rules/sc_rna_map.smk @@ -16,9 +16,9 @@ if config["platform"] == "10x-genomics": output: bam = "Result/STAR/{sample}/{sample}Aligned.sortedByCoord.out.bam", bai = "Result/STAR/{sample}/{sample}Aligned.sortedByCoord.out.bam.bai", - rawmtx = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/matrix.mtx", - feature = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/features.tsv", - barcode = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/barcodes.tsv" + rawmtx = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/matrix.mtx" %(config["STARsolo_Features"].split(" ")[0]), + feature = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/features.tsv" %(config["STARsolo_Features"].split(" ")[0]), + barcode = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/barcodes.tsv" %(config["STARsolo_Features"].split(" ")[0]) params: star_custom = config["STARsolo_Features"], outprefix = "Result/STAR/{sample}/{sample}", diff --git a/MAESTRO/Snakemake/scRNA/rules/sc_rna_merge.smk b/MAESTRO/Snakemake/scRNA/rules/sc_rna_merge.smk index e28541e..ee3d95b 100644 --- a/MAESTRO/Snakemake/scRNA/rules/sc_rna_merge.smk +++ b/MAESTRO/Snakemake/scRNA/rules/sc_rna_merge.smk @@ -1,8 +1,8 @@ rule scrna_merge: input: - rawmtx = expand("Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/matrix.mtx", sample=ALL_SAMPLES), - features = expand("Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/features.tsv", sample=ALL_SAMPLES)[1], - barcodes = expand("Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/barcodes.tsv", sample=ALL_SAMPLES) + rawmtx = expand("Result/STAR/{sample}/{sample}Solo.out/%s/raw/matrix.mtx" %(config["STARsolo_Features"].split(" ")[0]), sample=ALL_SAMPLES), + features = expand("Result/STAR/{sample}/{sample}Solo.out/%s/raw/features.tsv" %(config["STARsolo_Features"].split(" ")[0]), sample=ALL_SAMPLES)[1], + barcodes = expand("Result/STAR/{sample}/{sample}Solo.out/%s/raw/barcodes.tsv" %(config["STARsolo_Features"].split(" ")[0]), sample=ALL_SAMPLES) output: mergedmtx = "Result/STAR/%s/rawmatrix/matrix.mtx" % config["mergedname"], mergedfeatures = "Result/STAR/%s/rawmatrix/features.tsv" % config["mergedname"], diff --git a/MAESTRO/Snakemake/scRNA/rules/sc_rna_qc.smk b/MAESTRO/Snakemake/scRNA/rules/sc_rna_qc.smk index 9fa1e7c..0972ccd 100644 --- a/MAESTRO/Snakemake/scRNA/rules/sc_rna_qc.smk +++ b/MAESTRO/Snakemake/scRNA/rules/sc_rna_qc.smk @@ -1,9 +1,9 @@ if config["platform"] == "10x-genomics" or config["platform"] == "Dropseq": rule scrna_qc: input: - rawmtx = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/matrix.mtx", - feature = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/features.tsv", - barcode = "Result/STAR/{sample}/{sample}Solo.out/" + config["STARsolo_Features"] + "/raw/barcodes.tsv" + rawmtx = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/matrix.mtx" %(config["STARsolo_Features"].split(" ")[0]), + feature = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/features.tsv" %(config["STARsolo_Features"].split(" ")[0]), + barcode = "Result/STAR/{sample}/{sample}Solo.out/%s/raw/barcodes.tsv" %(config["STARsolo_Features"].split(" ")[0]) output: countgene = "Result/QC/{sample}/{sample}_count_gene_stat.txt", filtermatrix = "Result/QC/{sample}/{sample}_filtered_gene_count.h5",