From dbb4faac0653930346beda06152827f58c14064c Mon Sep 17 00:00:00 2001
From: Andrew Frantz <andrew.frantz@stjude.org>
Date: Fri, 9 Apr 2021 11:22:51 -0400
Subject: [PATCH] chore: bump to v1.0.1

---
 stjude_warden_bam/dxapp.json                                    | 2 +-
 .../internal_source/warden_bedgraph_to_bigwig/dxapp.json        | 2 +-
 .../app_data/internal_source/warden_bw_to_viewer/dxapp.json     | 2 +-
 .../app_data/internal_source/warden_combine_counts/dxapp.json   | 2 +-
 .../app_data/internal_source/warden_htseq_count/dxapp.json      | 2 +-
 .../warden_simple_differential_expression/dxapp.json            | 2 +-
 .../app_data/internal_source/warden_voom_limma/dxapp.json       | 2 +-
 stjude_warden_counts/dxapp.json                                 | 2 +-
 .../app_data/internal_source/warden_combine_counts/dxapp.json   | 2 +-
 .../warden_simple_differential_expression/dxapp.json            | 2 +-
 .../app_data/internal_source/warden_voom_limma/dxapp.json       | 2 +-
 stjude_warden_fastq/dxapp.json                                  | 2 +-
 .../internal_source/warden_bedgraph_to_bigwig/dxapp.json        | 2 +-
 .../app_data/internal_source/warden_bw_to_viewer/dxapp.json     | 2 +-
 .../app_data/internal_source/warden_combine_counts/dxapp.json   | 2 +-
 .../app_data/internal_source/warden_combine_flagstat/dxapp.json | 2 +-
 .../app_data/internal_source/warden_combine_sj_out/dxapp.json   | 2 +-
 .../resources/app_data/internal_source/warden_fastqc/dxapp.json | 2 +-
 .../app_data/internal_source/warden_htseq_count/dxapp.json      | 2 +-
 .../app_data/internal_source/warden_name_sort_bam/dxapp.json    | 2 +-
 .../warden_simple_differential_expression/dxapp.json            | 2 +-
 .../app_data/internal_source/warden_star_aligner/dxapp.json     | 2 +-
 .../app_data/internal_source/warden_voom_limma/dxapp.json       | 2 +-
 23 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/stjude_warden_bam/dxapp.json b/stjude_warden_bam/dxapp.json
index e1e4c95..4e6a53b 100644
--- a/stjude_warden_bam/dxapp.json
+++ b/stjude_warden_bam/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN [BAM] (St. Jude)",
   "summary": "This app runs htseq-count and voom/limma on RNA-SEQ data",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "BAM_FILES",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
index 0c5c22b..0ed2e8e 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Generate BigWig",
   "summary": "Generate BigWig files from bed coverage file",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "bedgraph_file",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
index 2d47ba5..4f486af 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: BigWig viewer",
   "summary": "Generate bookmarks to Protein Paint viewer for BigWig Files",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "viewer",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_combine_counts/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_combine_counts/dxapp.json
index 33bc294..807d5e5 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_combine_counts/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_combine_counts/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "count_files",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/dxapp.json
index 4a6cd62..5b75964 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: HTSeq-Count",
   "summary": "Generate per gene read (pair) counts",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_bam",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
index 6de89c2..818b323 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Simple Differential Expression",
   "summary": "Comparison between conditions.  Useful for when one condition has less three samples",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",
diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/dxapp.json
index a72135c..4009c34 100644
--- a/stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/dxapp.json
+++ b/stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",
diff --git a/stjude_warden_counts/dxapp.json b/stjude_warden_counts/dxapp.json
index aff1047..b82fd4a 100644
--- a/stjude_warden_counts/dxapp.json
+++ b/stjude_warden_counts/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN [Counts] (St. Jude)",
   "summary": "This app runs voom/limma differential expression on RNA-SEQ data",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "COUNT_FILES",
diff --git a/stjude_warden_counts/resources/app_data/internal_source/warden_combine_counts/dxapp.json b/stjude_warden_counts/resources/app_data/internal_source/warden_combine_counts/dxapp.json
index 33bc294..807d5e5 100644
--- a/stjude_warden_counts/resources/app_data/internal_source/warden_combine_counts/dxapp.json
+++ b/stjude_warden_counts/resources/app_data/internal_source/warden_combine_counts/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "count_files",
diff --git a/stjude_warden_counts/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/stjude_warden_counts/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
index 6de89c2..818b323 100644
--- a/stjude_warden_counts/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
+++ b/stjude_warden_counts/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Simple Differential Expression",
   "summary": "Comparison between conditions.  Useful for when one condition has less three samples",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",
diff --git a/stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/dxapp.json b/stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/dxapp.json
index a72135c..4009c34 100644
--- a/stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/dxapp.json
+++ b/stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",
diff --git a/stjude_warden_fastq/dxapp.json b/stjude_warden_fastq/dxapp.json
index 7f06819..3aff02b 100644
--- a/stjude_warden_fastq/dxapp.json
+++ b/stjude_warden_fastq/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN [FastQ] (St. Jude)",
   "summary": "This app runs the STAR Aligner, htseq-count, and voom/limma on RNA-SEQ data",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "FASTQ_FILES",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
index 0c5c22b..0ed2e8e 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_bedgraph_to_bigwig/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Generate BigWig",
   "summary": "Generate BigWig files from bed coverage file",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "bedgraph_file",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
index 2d47ba5..4f486af 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_bw_to_viewer/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: BigWig viewer",
   "summary": "Generate bookmarks to Protein Paint viewer for BigWig Files",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "viewer",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_counts/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_counts/dxapp.json
index 33bc294..807d5e5 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_counts/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_counts/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "count_files",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_flagstat/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_flagstat/dxapp.json
index 84314ac..04c4ff2 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_flagstat/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_flagstat/dxapp.json
@@ -3,7 +3,7 @@
   "title": "warden_combine_flagstat",
   "summary": "warden_combine_flagstat",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "flagstat_files",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_sj_out/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_sj_out/dxapp.json
index b8f0626..23a8dc6 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_sj_out/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_combine_sj_out/dxapp.json
@@ -3,7 +3,7 @@
   "title": "warden_combine_sj_out",
   "summary": "warden_combine_sj_out",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "sj_out_files",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_fastqc/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_fastqc/dxapp.json
index f07d46b..2a6c7f2 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_fastqc/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_fastqc/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: FASTQC",
   "summary": "FASTQC Analysis",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "fastq_input",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/dxapp.json
index 4a6cd62..5b75964 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: HTSeq-Count",
   "summary": "Generate per gene read (pair) counts",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_bam",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_name_sort_bam/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_name_sort_bam/dxapp.json
index d8a2473..932be15 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_name_sort_bam/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_name_sort_bam/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Sort BAM by name",
   "summary": "BAM Output generated in alignment phase is sorted by read name for analysis by HTSeq-count",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_bam",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
index 6de89c2..818b323 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Simple Differential Expression",
   "summary": "Comparison between conditions.  Useful for when one condition has less three samples",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_star_aligner/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_star_aligner/dxapp.json
index 0fc5a46..0963c5f 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_star_aligner/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_star_aligner/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: STAR Aligner",
   "summary": "Runs the STAR alignment program on input data",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "read_file1",
diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/dxapp.json
index a72135c..4009c34 100644
--- a/stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/dxapp.json
+++ b/stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "inputSpec": [
     {
       "name": "input_count_file",