fix rule align (star) parameters and make gtf an actual input

snakemake-workflows · Apr 19, 2023 · fdce847 · fdce847
1 parent 9bb366c
commit fdce847
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -59,4 +59,4 @@ diffexp:
 params:
   cutadapt-pe: ""
   cutadapt-se: ""
-  star: "--outSAMtype BAM Unsorted"
+  star: ""
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -2,16 +2,15 @@ rule align:
     input:
         unpack(get_fq),
         index="resources/star_genome",
+        gtf="resources/genome.gtf"
     output:
         aln="results/star/{sample}_{unit}/Aligned.sortedByCoord.out.bam",
         reads_per_gene="results/star/{sample}_{unit}/ReadsPerGene.out.tab",
     log:
         "logs/star/{sample}_{unit}.log",
     params:
         idx=lambda wc, input: input.index,
-        extra="--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile {} {}".format(
-            "resources/genome.gtf", config["params"]["star"]
-        ),
+        extra=lambda wc, input: f'--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile {input.gtf} {config["params"]["star"]}',
     threads: 24
     wrapper:
         "v1.21.4/bio/star/align"