Update references to rnaseq-standard/v2.1.0

stjudecloud · Mar 31, 2021 · 70c39cb · 70c39cb
1 parent 3bc1fc7
commit 70c39cb
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Showing 12 changed files with 48 additions and 48 deletions.
diff --git 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/v2.0.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/fq.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/picard.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fq.wdl"
 
 workflow bam_to_fastqs {
     input {

diff --git a/workflows/general/bwa-db-build.wdl b/workflows/general/bwa-db-build.wdl
@@ -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/wget.wdl"
+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"
 
 workflow bwa_db_build {
     input {

diff --git a/workflows/qc/make-qc-reference.wdl b/workflows/qc/make-qc-reference.wdl
@@ -4,12 +4,12 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/fastq_screen.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/fastq_screen.wdl"
 
 workflow make_qc_reference {
     call fastq_screen.build_db as fastq_screen_build_db
 
     output {
         File fastq_screen_db = fastq_screen_build_db.db
     }
-}
+}
diff --git 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/v2.0.0/tools/md5sum.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/fastqc.wdl" as fqc
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/qualimap.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/fq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/fastq_screen.wdl" as fq_screen
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/multiqc.wdl" as mqc
+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
 
 workflow quality_check {
     input {

diff --git a/workflows/rnaseq/ESTIMATE.wdl b/workflows/rnaseq/ESTIMATE.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/estimate.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/estimate.wdl"
 
 workflow ESTIMATE {
     input {

diff --git 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/master/tools/util.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.1.0/tools/util.wdl"
 
 workflow calc_gene_lengths {
     input {

diff --git a/workflows/rnaseq/rnaseq-standard-fastq.wdl b/workflows/rnaseq/rnaseq-standard-fastq.wdl
@@ -28,15 +28,15 @@
 
 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/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/master/tools/deeptools.wdl"
-import "https://raw.githubusercontent.com/stjude/xenocp/master/wdl/workflows/xenocp.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/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/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl"
 
 workflow rnaseq_standard_fastq {
     input {

diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl
@@ -30,15 +30,15 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/workflows/general/bam-to-fastqs.wdl" as b2fq
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/picard.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/deeptools.wdl"
-import "https://raw.githubusercontent.com/stjude/xenocp/master/wdl/workflows/xenocp.wdl"
+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/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl"
 
 workflow rnaseq_standard {
     input {

diff --git 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/v2.0.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/wget.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/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
@@ -37,9 +37,9 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/workflows/rnaseq/rnaseq-standard.wdl" as rnav2
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/tsne.wdl"
+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"
 
 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
@@ -36,11 +36,11 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/htseq.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/samtools.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/ngsderive.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/tsne.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/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"
 
 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
@@ -34,8 +34,8 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/util.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v2.0.0/tools/tsne.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"
 
 workflow rnaseq_expression_classification_from_counts {
     input {