chore: point to this release

Author: a-frantz

workflows/general/bwa-db-build.wdl

@@ -33,8 +33,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/bwa.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/bwa.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
 
 workflow bwa_db_build {
     input {

workflows/qc/quality-check-standard.wdl

@@ -27,16 +27,16 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/md5sum.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/fastqc.wdl" as fqc
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/qualimap.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/fq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/fastq_screen.wdl" as fq_screen
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/sequencerr.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/multiqc.wdl" as mqc
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/md5sum.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fastqc.wdl" as fqc
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/qualimap.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fastq_screen.wdl" as fq_screen
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/sequencerr.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/multiqc.wdl" as mqc
 
 workflow quality_check {
     input {

workflows/rnaseq/rnaseq-standard-fastq.wdl

@@ -28,13 +28,13 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/fq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/deeptools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/htseq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/deeptools.wdl"
 import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl" as xenocp_workflow
 
 workflow rnaseq_standard_fastq {

workflows/rnaseq/rnaseq-standard.wdl

@@ -30,14 +30,14 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/workflows/general/bam-to-fastqs.wdl" as b2fq
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/deeptools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/workflows/general/bam-to-fastqs.wdl" as b2fq
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/htseq.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/deeptools.wdl"
 import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl" as xenocp_workflow
 
 workflow rnaseq_standard {

workflows/rnaseq/rnaseq-star-db-build.wdl

@@ -36,8 +36,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
 
 workflow rnaseq_star_db_build {
     input {