From 3ada40553141194d3b0c73b44739b922076ef6c1 Mon Sep 17 00:00:00 2001 From: SamBryce-Smith Date: Fri, 24 May 2024 09:55:02 +0100 Subject: [PATCH] fix bam idx paths --- rules/rseqc.smk | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/rules/rseqc.smk b/rules/rseqc.smk index 83e0ca3..a351d55 100644 --- a/rules/rseqc.smk +++ b/rules/rseqc.smk @@ -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") @@ -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") @@ -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") @@ -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")