chore: bump to v1.2.0

stjude · Nov 20, 2023 · fe3c03a · fe3c03a
1 parent 00648ca
commit fe3c03a
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Showing 37 changed files with 37 additions and 37 deletions.
diff --git 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": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: Generate BigWig",
   "summary": "Generate BigWig files from bed coverage file",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: BigWig viewer",
   "summary": "Generate bookmarks to Protein Paint viewer for BigWig Files",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "viewer",

diff --git a/...den_bam/resources/app_data/internal_source/warden_bw_to_viewer/src/warden_bw_to_viewer.sh b/...den_bam/resources/app_data/internal_source/warden_bw_to_viewer/src/warden_bw_to_viewer.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # shellcheck disable=SC2154
-# warden_bw_to_viewer 1.1.0
+# warden_bw_to_viewer 1.2.0
 set -e -o -x
 
 main() {

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "count_files",

diff --git a/stjude_warden_bam/resources/app_data/internal_source/warden_genome_coverage_bed/dxapp.json b/stjude_warden_bam/resources/app_data/internal_source/warden_genome_coverage_bed/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Genome coverage analysis",
   "summary": "Creates coverage files (BED) of alignment files (BAM)",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_bam",

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: HTSeq-Count",
   "summary": "Generate per gene read (pair) counts",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_bam",

diff --git a/...n_bam/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/...n_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": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh b/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_simple_differential_expression 1.1.0
+# warden_simple_differential_expression 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/..._warden_bam/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh b/..._warden_bam/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_voom_limma 1.1.0
+# warden_voom_limma 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

diff --git a/stjude_warden_bam/resources/usr/bin/create_workflow.py b/stjude_warden_bam/resources/usr/bin/create_workflow.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# warden_python 1.1.0
+# warden_python 1.2.0
 
 
 import sys

diff --git 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": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "count_files",

diff --git a/...ounts/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/...ounts/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": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh b/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_simple_differential_expression 1.1.0
+# warden_simple_differential_expression 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/...rden_counts/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh b/...rden_counts/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_voom_limma 1.1.0
+# warden_voom_limma 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

diff --git a/stjude_warden_counts/resources/usr/bin/create_workflow.py b/stjude_warden_counts/resources/usr/bin/create_workflow.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# warden_python 1.1.0
+# warden_python 1.2.0
 
 
 import sys

diff --git 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": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: Generate BigWig",
   "summary": "Generate BigWig files from bed coverage file",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: BigWig viewer",
   "summary": "Generate bookmarks to Protein Paint viewer for BigWig Files",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "viewer",

diff --git a/...n_fastq/resources/app_data/internal_source/warden_bw_to_viewer/src/warden_bw_to_viewer.sh b/...n_fastq/resources/app_data/internal_source/warden_bw_to_viewer/src/warden_bw_to_viewer.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # shellcheck disable=SC2154
-# warden_bw_to_viewer 1.1.0
+# warden_bw_to_viewer 1.2.0
 set -e -o -x
 
 main() {

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: Combine HTSeq Counts",
   "summary": "Combine HTSeq Count files into a single file",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "warden_combine_flagstat",
   "summary": "warden_combine_flagstat",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "warden_combine_sj_out",
   "summary": "warden_combine_sj_out",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "sj_out_files",

diff --git a/...stq/resources/app_data/internal_source/warden_combine_sj_out/src/warden_combine_sj_out.sh b/...stq/resources/app_data/internal_source/warden_combine_sj_out/src/warden_combine_sj_out.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # shellcheck disable=SC2154
-# warden_combine_sj_out 1.1.0
+# warden_combine_sj_out 1.2.0
 
 main() {
     wget -nv "https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary"

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: FASTQC",
   "summary": "FASTQC Analysis",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "fastq_input",

diff --git a/stjude_warden_fastq/resources/app_data/internal_source/warden_genome_coverage_bed/dxapp.json b/stjude_warden_fastq/resources/app_data/internal_source/warden_genome_coverage_bed/dxapp.json
@@ -3,7 +3,7 @@
   "title": "WARDEN: Genome coverage analysis",
   "summary": "Creates coverage files (BED) of alignment files (BAM)",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_bam",

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: HTSeq-Count",
   "summary": "Generate per gene read (pair) counts",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -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": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_bam",

diff --git a/...fastq/resources/app_data/internal_source/warden_simple_differential_expression/dxapp.json b/...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": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh b/...source/warden_simple_differential_expression/src/warden_simple_differential_expression.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_simple_differential_expression 1.1.0
+# warden_simple_differential_expression 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

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
@@ -3,7 +3,7 @@
   "title": "WARDEN: STAR Aligner",
   "summary": "Runs the STAR alignment program on input data",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "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
@@ -3,7 +3,7 @@
   "title": "WARDEN: LIMMA",
   "summary": "Run VOOM normalization and LIMMA analysis",
   "dxapi": "1.0.0",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "inputSpec": [
     {
       "name": "input_count_file",

diff --git a/...arden_fastq/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh b/...arden_fastq/resources/app_data/internal_source/warden_voom_limma/src/warden_voom_limma.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# warden_voom_limma 1.1.0
+# warden_voom_limma 1.2.0
 # shellcheck disable=SC2154
 set -e -x -o
 

diff --git a/stjude_warden_fastq/resources/usr/bin/create_workflow.py b/stjude_warden_fastq/resources/usr/bin/create_workflow.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# warden_python 1.1.0
+# warden_python 1.2.0
 
 
 import sys