From 361c65714f7cea3e19f3586f19fb4b22603d708a Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Wed, 31 May 2023 13:39:07 -0700 Subject: [PATCH 1/3] Add parameter meta, remove unused variable --- assembly/wdl/tasks/down_sampling.wdl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/assembly/wdl/tasks/down_sampling.wdl b/assembly/wdl/tasks/down_sampling.wdl index b740e2a0..dd545943 100755 --- a/assembly/wdl/tasks/down_sampling.wdl +++ b/assembly/wdl/tasks/down_sampling.wdl @@ -8,7 +8,13 @@ workflow RunDownSampling{ Float downsampledCoverage Float refLength = 3100000000.0 File? referenceFasta - Int fileExtractionDiskSizeGB = 256 + } + + parameter_meta { + readFiles: "Reads file in BAM, FASTQ, or FASTA format (optionally gzipped)", + downsampledCoverage: "Target coverage after downsampling", + refLength: "Length of reference genome in bytes", + referenceFasta: "Fasta of reference genome" } scatter (readFile in readFiles){ From 537963fcc69b1e4d3b80cb92d58a886b85f95641 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Wed, 31 May 2023 13:40:03 -0700 Subject: [PATCH 2/3] Fix typo --- assembly/wdl/tasks/down_sampling.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assembly/wdl/tasks/down_sampling.wdl b/assembly/wdl/tasks/down_sampling.wdl index dd545943..c8269f2a 100755 --- a/assembly/wdl/tasks/down_sampling.wdl +++ b/assembly/wdl/tasks/down_sampling.wdl @@ -11,7 +11,7 @@ workflow RunDownSampling{ } parameter_meta { - readFiles: "Reads file in BAM, FASTQ, or FASTA format (optionally gzipped)", + readFiles: "Reads files in BAM, CRAM, FASTQ, or FASTA format (optionally gzipped)", downsampledCoverage: "Target coverage after downsampling", refLength: "Length of reference genome in bytes", referenceFasta: "Fasta of reference genome" From 935c21f2168fcec0db2a92929ada76d37d526e79 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Wed, 31 May 2023 13:58:49 -0700 Subject: [PATCH 3/3] Clarify len(ref) != refLength --- assembly/wdl/tasks/down_sampling.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assembly/wdl/tasks/down_sampling.wdl b/assembly/wdl/tasks/down_sampling.wdl index c8269f2a..72224ed0 100755 --- a/assembly/wdl/tasks/down_sampling.wdl +++ b/assembly/wdl/tasks/down_sampling.wdl @@ -14,7 +14,7 @@ workflow RunDownSampling{ readFiles: "Reads files in BAM, CRAM, FASTQ, or FASTA format (optionally gzipped)", downsampledCoverage: "Target coverage after downsampling", refLength: "Length of reference genome in bytes", - referenceFasta: "Fasta of reference genome" + referenceFasta: "Fasta of reference genome (does not override refLength)" } scatter (readFile in readFiles){