fix path when feeding multi parameters to --STARsolo Features

liulab-dfci · Jul 23, 2021 · 76ec524 · 76ec524
1 parent 09bdd7f
commit 76ec524
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git 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
@@ -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
@@ -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",