Merge pull request #105 from Cristianetaniguti/develop

Develop
Cristianetaniguti · Jul 13, 2023 · a202c7c · a202c7c
2 parents 25aa852 + c42316e
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diff --git 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., &#38; 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/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
@@ -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

diff --git 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" \

diff --git 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
@@ -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 <<<