diff --git a/workflows/general/bam-to-fastqs.wdl b/workflows/general/bam-to-fastqs.wdl
index 7444be4f4..12e8f4b19 100644
--- a/workflows/general/bam-to-fastqs.wdl
+++ b/workflows/general/bam-to-fastqs.wdl
@@ -35,9 +35,9 @@
 version 1.0
 
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
 
 workflow bam_to_fastqs {
     input {
diff --git a/workflows/general/bwa-db-build.wdl b/workflows/general/bwa-db-build.wdl
index 9215a9181..3c5190f16 100644
--- a/workflows/general/bwa-db-build.wdl
+++ b/workflows/general/bwa-db-build.wdl
@@ -33,8 +33,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/bwa.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/wget.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/bwa.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/wget.wdl"
 
 workflow bwa_db_build {
     input {
diff --git a/workflows/qc/make-qc-reference.wdl b/workflows/qc/make-qc-reference.wdl
index 5289c4412..2efe636c3 100644
--- a/workflows/qc/make-qc-reference.wdl
+++ b/workflows/qc/make-qc-reference.wdl
@@ -4,7 +4,7 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fastq_screen.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastq_screen.wdl"
 
 workflow make_qc_reference {
     call fastq_screen.build_db as fastq_screen_build_db
diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl
index ddd59c86f..e0de371a8 100644
--- a/workflows/qc/quality-check-standard.wdl
+++ b/workflows/qc/quality-check-standard.wdl
@@ -27,15 +27,15 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/md5sum.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fastqc.wdl" as fqc
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/qualimap.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fastq_screen.wdl" as fq_screen
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/multiqc.wdl" as mqc
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/md5sum.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastqc.wdl" as fqc
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/qualimap.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastq_screen.wdl" as fq_screen
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/multiqc.wdl" as mqc
 
 workflow quality_check {
     input {
diff --git a/workflows/rnaseq/ESTIMATE.wdl b/workflows/rnaseq/ESTIMATE.wdl
index 9fdf251ed..fa6d01f2e 100644
--- a/workflows/rnaseq/ESTIMATE.wdl
+++ b/workflows/rnaseq/ESTIMATE.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/estimate.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/estimate.wdl"
 
 workflow ESTIMATE {
     input {
diff --git a/workflows/rnaseq/calc-gene-lengths.wdl b/workflows/rnaseq/calc-gene-lengths.wdl
index 8cb9300b4..609faf9a6 100644
--- a/workflows/rnaseq/calc-gene-lengths.wdl
+++ b/workflows/rnaseq/calc-gene-lengths.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
 
 workflow calc_gene_lengths {
     input {
diff --git a/workflows/rnaseq/rnaseq-standard-fastq.wdl b/workflows/rnaseq/rnaseq-standard-fastq.wdl
index 5ba8cb8f5..7f438e175 100644
--- a/workflows/rnaseq/rnaseq-standard-fastq.wdl
+++ b/workflows/rnaseq/rnaseq-standard-fastq.wdl
@@ -28,14 +28,14 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/deeptools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/deeptools.wdl"
 import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl"
 
 workflow rnaseq_standard_fastq {
diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl
index 733dc6856..0c25ea98d 100755
--- a/workflows/rnaseq/rnaseq-standard.wdl
+++ b/workflows/rnaseq/rnaseq-standard.wdl
@@ -30,14 +30,14 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/workflows/general/bam-to-fastqs.wdl" as b2fq
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/deeptools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/workflows/general/bam-to-fastqs.wdl" as b2fq
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/deeptools.wdl"
 import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl"
 
 workflow rnaseq_standard {
diff --git a/workflows/rnaseq/rnaseq-star-db-build.wdl b/workflows/rnaseq/rnaseq-star-db-build.wdl
index dba631d1d..52dd7aa16 100644
--- a/workflows/rnaseq/rnaseq-star-db-build.wdl
+++ b/workflows/rnaseq/rnaseq-star-db-build.wdl
@@ -36,8 +36,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/wget.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/wget.wdl"
 
 workflow rnaseq_star_db_build {
     input {
diff --git a/workflows/rnaseq_expression_classification/rnaseq_expression_classification.wdl b/workflows/rnaseq_expression_classification/rnaseq_expression_classification.wdl
index 3cb3bda7b..505b0e4c1 100644
--- a/workflows/rnaseq_expression_classification/rnaseq_expression_classification.wdl
+++ b/workflows/rnaseq_expression_classification/rnaseq_expression_classification.wdl
@@ -37,9 +37,9 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/workflows/rnaseq/rnaseq-standard.wdl" as rnav2
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/tsne.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/workflows/rnaseq/rnaseq-standard.wdl" as rnav2
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
 
 workflow rnaseq_expression_classification {
     input { 
diff --git a/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_bams.wdl b/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_bams.wdl
index 3b3d082dd..a3a1de670 100644
--- a/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_bams.wdl
+++ b/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_bams.wdl
@@ -36,11 +36,11 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/tsne.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
 
 workflow rnaseq_expression_classification_from_bams {
     input { 
diff --git a/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_counts.wdl b/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_counts.wdl
index c9108b3cd..24642e72b 100644
--- a/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_counts.wdl
+++ b/workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_counts.wdl
@@ -34,8 +34,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/tsne.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
 
 workflow rnaseq_expression_classification_from_counts {
     input {