From 1c691d190b9910786777794491125eabfc111fb1 Mon Sep 17 00:00:00 2001 From: Yueyao Gao Date: Mon, 17 Jun 2024 17:23:21 -0400 Subject: [PATCH] updated the plot output name in WDL --- CoverageProfiler/CoverageProfiler.wdl | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl index 69073b4..7f63da9 100644 --- a/CoverageProfiler/CoverageProfiler.wdl +++ b/CoverageProfiler/CoverageProfiler.wdl @@ -195,18 +195,18 @@ workflow coverageProfile { -g ~{GCcontentTrack} \ -o output - mv output/*_samtools_cov_with_gc.png output/sample_coverage_profile.png - mv output/*_avg_cov_per_chr.png output/avg_cov_per_chr.png - mv output/*_avg_cov_std.txt output/per_chr_cov_std.txt - mv output/*_avg_cov_per_chr.csv output/per_chr_avg_cov.csv - mv output/*_avg_cov_mean.txt output/avg_cov_mean.txt + mv output/*_samtools_cov_with_gc.png output/~{sampleName}_sample_coverage_profile.png + mv output/*_avg_cov_per_chr.png output/~{sampleName}_avg_cov_per_chr.png + mv output/*_avg_cov_std.txt output/~{sampleName}_per_chr_cov_std.txt + mv output/*_avg_cov_per_chr.csv output/~{sampleName}_per_chr_avg_cov.csv + mv output/*_avg_cov_mean.txt output/~{sampleName}_avg_cov_mean.txt >>> output { - File cov_profile_plot = "output/sample_coverage_profile.png" - File avg_chr_cov_per_chr_plot = "output/avg_cov_per_chr.png" - Float avg_chr_cov_std = read_float("output/per_chr_cov_std.txt") - File avg_chr_cov_per_chr = "output/per_chr_avg_cov.csv" - Float avg_cov_mean = read_float("output/avg_cov_mean.txt") + File cov_profile_plot = "output/~{sampleName}_sample_coverage_profile.png" + File avg_chr_cov_per_chr_plot = "output/~{sampleName}_avg_cov_per_chr.png" + Float avg_chr_cov_std = read_float("output/~{sampleName}_per_chr_cov_std.txt") + File avg_chr_cov_per_chr = "output/~{sampleName}_per_chr_avg_cov.csv" + Float avg_cov_mean = read_float("output/~{sampleName}_avg_cov_mean.txt") } runtime { memory: select_first([mem_gb, 7]) * 1000 + " MB"