From 2134d8d9ecbf727e2f8889a0e2c1a087f181df28 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 00:13:30 +0000 Subject: [PATCH 01/10] change disk size variable to int change disk size variable to int --- .../checker-workflow-wrapping-alignment-workflow.wdl | 4 ++-- functional-equivalence-checker/topmed-alignment-checker.wdl | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index ca13b24..77f9b22 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -38,7 +38,7 @@ workflow checkerWorkflow { Int agg_preemptible_tries # Get the size of the standard reference files - Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + Int ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") call TopMed_aligner.PairedEndSingleSampleWorkflow as aligner { input: @@ -77,7 +77,7 @@ workflow checkerWorkflow { } - Float total_size = ref_size + size(aligner.output_cram, "GB") + Int total_size = ref_size + size(aligner.output_cram, "GB") call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, total_size=total_size } } diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index 2b4ba05..67e5855 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -3,7 +3,7 @@ task checkerTask { File referenceFasta Int expectedNumofReads File docker_image - Float total_size + Int total_size command { printf "The CRAM file is ${inputCRAMFile}" @@ -29,6 +29,6 @@ task checkerTask { runtime { docker: docker_image - disk_size = total_size + disks: "local-disk " + total_size + " HDD" } } From e1a0c64d98d5f78fe7959a716e5e0ad055e7b7b9 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 00:22:57 +0000 Subject: [PATCH 02/10] fix the disk runtime section and the type for the disk size fix the disk runtime section and the type for the disk size --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 77f9b22..27b5799 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -1,5 +1,5 @@ import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/topmed-firecloud-demo/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner -import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/develop/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker +import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/feature/checker-fix/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker workflow checkerWorkflow { #File referenceFasta From 2459fbd84eb6a8e1f952e5a58896d2c421174569 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 00:31:23 +0000 Subject: [PATCH 03/10] fix disk size to Float fix disk size to Float --- .../checker-workflow-wrapping-alignment-workflow.wdl | 4 ++-- functional-equivalence-checker/topmed-alignment-checker.wdl | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 27b5799..11ba7bc 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -77,7 +77,7 @@ workflow checkerWorkflow { } - Int total_size = ref_size + size(aligner.output_cram, "GB") + Float disk__size = ref_size + size(aligner.output_cram, "GB") - call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, total_size=total_size } + call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, disk_size=disk_size } } diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index 67e5855..bc6d066 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -3,7 +3,7 @@ task checkerTask { File referenceFasta Int expectedNumofReads File docker_image - Int total_size + Float disk_size command { printf "The CRAM file is ${inputCRAMFile}" @@ -29,6 +29,6 @@ task checkerTask { runtime { docker: docker_image - disks: "local-disk " + total_size + " HDD" + disks: "local-disk " + sub(disk_size, "\\..*", "") + " HDD" } } From 95b3a09c3af54b33c5ed9f6a9bc9d0f20448eb60 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 00:34:23 +0000 Subject: [PATCH 04/10] fix ref_size to Float fix ref_size to Float --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 11ba7bc..698d24a 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -38,7 +38,7 @@ workflow checkerWorkflow { Int agg_preemptible_tries # Get the size of the standard reference files - Int ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") call TopMed_aligner.PairedEndSingleSampleWorkflow as aligner { input: From 60ed7cde7e7fa9bd5992a7418e221303b54c1e07 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 15:41:32 +0000 Subject: [PATCH 05/10] fix the disk size variable fix the disk size variable --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 698d24a..7a5161f 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -77,7 +77,7 @@ workflow checkerWorkflow { } - Float disk__size = ref_size + size(aligner.output_cram, "GB") + Float disk_size = ref_size + size(aligner.output_cram, "GB") call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, disk_size=disk_size } } From e8cc5b049890d14ab41ee0c5e42506ccf789a03d Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 17:17:38 +0000 Subject: [PATCH 06/10] make docker_image a String make docker_image a String --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- functional-equivalence-checker/topmed-alignment-checker.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 7a5161f..3044b05 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -4,7 +4,7 @@ import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/feature workflow checkerWorkflow { #File referenceFasta Int expectedNumofReads - File docker_image + String docker_image File wgs_evaluation_interval_list File wgs_coverage_interval_list diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index bc6d066..5e6ba7d 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -2,7 +2,7 @@ task checkerTask { File inputCRAMFile File referenceFasta Int expectedNumofReads - File docker_image + String docker_image Float disk_size command { From 070a18ecfff4cb5f0c159a00f1e49e378b32ec1f Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 21:34:52 +0000 Subject: [PATCH 07/10] remove reference from checker WDL because it is not needed --- .../checker-workflow-wrapping-alignment-workflow.wdl | 6 +----- functional-equivalence-checker/topmed-alignment-checker.wdl | 3 ++- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 3044b05..e6c58b2 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -37,9 +37,6 @@ workflow checkerWorkflow { Int preemptible_tries Int agg_preemptible_tries - # Get the size of the standard reference files - Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB") - call TopMed_aligner.PairedEndSingleSampleWorkflow as aligner { input: #docker_image = docker_image, @@ -77,7 +74,6 @@ workflow checkerWorkflow { } - Float disk_size = ref_size + size(aligner.output_cram, "GB") - call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, disk_size=disk_size } + call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, expectedNumofReads=expectedNumofReads, docker_image=docker_image, disk_size=disk_size } } diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index 5e6ba7d..889d78c 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -1,10 +1,11 @@ task checkerTask { File inputCRAMFile - File referenceFasta Int expectedNumofReads String docker_image Float disk_size + Float disk_size = size(inputCRAMFile, "GB") + command { printf "The CRAM file is ${inputCRAMFile}" samtools flagstat ${inputCRAMFile} > cram_flagstat.txt From ea2fa88a33e616ca233099f09856180f2654d5a9 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 21:40:17 +0000 Subject: [PATCH 08/10] fix multiple declaration of disk_size --- functional-equivalence-checker/topmed-alignment-checker.wdl | 1 - 1 file changed, 1 deletion(-) diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl index 889d78c..1343d13 100644 --- a/functional-equivalence-checker/topmed-alignment-checker.wdl +++ b/functional-equivalence-checker/topmed-alignment-checker.wdl @@ -2,7 +2,6 @@ task checkerTask { File inputCRAMFile Int expectedNumofReads String docker_image - Float disk_size Float disk_size = size(inputCRAMFile, "GB") From c1ad7b755a6662a2b16a9a9d58d484765ff8a486 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 26 Apr 2018 21:42:01 +0000 Subject: [PATCH 09/10] disk size computed in topmed checker --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index e6c58b2..03885d7 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -75,5 +75,5 @@ workflow checkerWorkflow { } - call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, expectedNumofReads=expectedNumofReads, docker_image=docker_image, disk_size=disk_size } + call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, expectedNumofReads=expectedNumofReads, docker_image=docker_image} } From 2b693b6084a0bd16c82b8ea5f1809b485c565186 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Mon, 30 Apr 2018 20:58:00 +0000 Subject: [PATCH 10/10] base WDL for checker tool on a release tag --- .../checker-workflow-wrapping-alignment-workflow.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl index 03885d7..d2a5014 100644 --- a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl +++ b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl @@ -1,5 +1,5 @@ import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/topmed-firecloud-demo/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner -import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/feature/checker-fix/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker +import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.4.0/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker workflow checkerWorkflow { #File referenceFasta