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rseqc.smk - fix BAM index file names in input #60

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8 changes: 4 additions & 4 deletions rules/rseqc.smk
Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ rule all_rseqc:
rule infer_experiment:
input:
bam = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam"),
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam")
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam.bai")

output:
os.path.join(RSEQC_OUTDIR, "{sample}.infer_experiment.txt")
Expand All @@ -107,7 +107,7 @@ rule infer_experiment:
rule inner_distance_freq:
input:
bam = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam"),
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam")
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam.bai")

output:
os.path.join(RSEQC_OUTDIR, "{sample}.inner_distance_freq.txt")
Expand All @@ -130,7 +130,7 @@ rule inner_distance_freq:
rule junction_saturation:
input:
bam = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam"),
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam")
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam.bai")

output:
os.path.join(RSEQC_OUTDIR, "{sample}.junctionSaturation_plot.r")
Expand All @@ -153,7 +153,7 @@ rule junction_saturation:
rule read_distribution:
input:
bam = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam"),
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam")
idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam.bai")

output:
os.path.join(RSEQC_OUTDIR, "{sample}.read_distribution.txt")
Expand Down