From a3dfc4d545fabe16850b700c4b1e9dd742550fe8 Mon Sep 17 00:00:00 2001 From: cristianetaniguti Date: Tue, 11 Jul 2023 16:38:12 -0500 Subject: [PATCH 1/3] change gatk max_mem --- README.md | 2 +- tasks/gatk.wdl | 6 +++--- tasks/stacks.wdl | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index e384d08..a573bf5 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,7 @@ Check how to evaluate the workflows results in Reads2MapApp Shiny (so far only a Check more information and examples of usage in: -* [Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Mollinari, M., Da, G., Pereira, S., Riera-Lizarazu, O., Lau, J., Byrne, D., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., & Franco Garcia, A. A. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847](https://www.biorxiv.org/content/10.1101/2022.11.24.517847v2) +* [Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847](https://www.biorxiv.org/content/10.1101/2022.11.24.517847v3) ## Third-party software and images diff --git a/tasks/gatk.wdl b/tasks/gatk.wdl index ca3e714..4c8fe8c 100644 --- a/tasks/gatk.wdl +++ b/tasks/gatk.wdl @@ -16,8 +16,8 @@ task HaplotypeCaller { } Int disk_size = ceil((size(bams, "GiB") + 30) + size(reference_fasta, "GiB")) + 20 - Int memory_max = ceil(max_ram/chunk_size - 1000) Int memory_min = ceil((max_ram/chunk_size)/5) + Int memory_max = ceil(max_ram/chunk_size - memory_min) Int memory_size = max_ram Int max_cores = ceil(chunk_size * 4 + 2) @@ -81,8 +81,8 @@ task ImportGVCFs { } Int disk_size = ceil(size(vcfs, "GiB") * 1.5 + size(reference_fasta, "GiB") * 1.5) - Int memory_max = ceil(max_ram - 1000) Int memory_min = ceil(max_ram/3.85) + Int memory_max = ceil(max_ram - memory_min) Int memory_size = max_ram command <<< @@ -139,8 +139,8 @@ task GenotypeGVCFs { } Int disk_size = ceil(size(reference_fasta, "GiB") * 1.5 + size(workspace_tar, "GiB") * 1.5) - Int memory_max = ceil(max_ram - 1000) Int memory_min = ceil(max_ram/3.85) + Int memory_max = ceil(max_ram - memory_min) Int memory_size = max_ram command <<< diff --git a/tasks/stacks.wdl b/tasks/stacks.wdl index e2fa5fb..9244c80 100644 --- a/tasks/stacks.wdl +++ b/tasks/stacks.wdl @@ -92,7 +92,7 @@ task RefMap { } Int disk_size = ceil(size(bams, "GiB") * 2) - Int memory_size = 4000 + ceil(size(bams, "MiB") * 2) + Int memory_size = 3000 + ceil(size(bams, "MiB") * 2) command <<< From 971c45ae8240f5471448f588f8ef4d4c3baaa4b4 Mon Sep 17 00:00:00 2001 From: cristianetaniguti Date: Thu, 13 Jul 2023 16:49:55 -0500 Subject: [PATCH 2/3] fix pair-end example --- tasks/BWA.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/BWA.wdl b/tasks/BWA.wdl index 86129ff..fe85c62 100644 --- a/tasks/BWA.wdl +++ b/tasks/BWA.wdl @@ -40,7 +40,7 @@ task RunBwaAlignment { fi bwa_header="@RG\tID:${sampleName_list[$index]}.${lib_list[$index]}\tLB:lib-${lib_list[$index]}\tPL:illumina\tSM:${sampleName_list[$index]}\tPU:FLOWCELL1.LANE1.${lib_list[$index]}" - /usr/gitc/./bwa mem -t ~{max_cores} -R "${bwa_header}" ~{references.ref_fasta} "$reads" | \ + /usr/gitc/./bwa mem -t ~{max_cores} -R "${bwa_header}" ~{references.ref_fasta} $reads | \ java -jar /usr/gitc/picard.jar SortSam \ I=/dev/stdin \ O="${sampleName_list[$index]}.${lib_list[$index]}.sorted.bam" \ From c42316e6426ded1edab384b81a50e263c687babd Mon Sep 17 00:00:00 2001 From: cristianetaniguti Date: Thu, 13 Jul 2023 16:53:06 -0500 Subject: [PATCH 3/3] up versions --- pipelines/EmpiricalReads2Map/EmpiricalReads2Map.changelog.md | 4 ++++ .../EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/pipelines/EmpiricalReads2Map/EmpiricalReads2Map.changelog.md b/pipelines/EmpiricalReads2Map/EmpiricalReads2Map.changelog.md index efedf23..ae5b43a 100644 --- a/pipelines/EmpiricalReads2Map/EmpiricalReads2Map.changelog.md +++ b/pipelines/EmpiricalReads2Map/EmpiricalReads2Map.changelog.md @@ -1,3 +1,7 @@ +# 1.4.3 + +* Update example for pair-end reads inputs + # 1.4.2 * more flexibility to choose the probability to be used in the HMM: diff --git a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md index 051d0ee..07e2c36 100644 --- a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md +++ b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md @@ -1,3 +1,7 @@ +# 1.4.2 + +* Update example for pair-end reads inputs + # 1.4.1 * Use BCFtools norm to left-align indel marker positions identified by GATK, STACKs and freebayes