Merge pull request #36 from uclahs-cds/sfitz-rename-and-release

Rename pipeline and first release
uclahs-cds · Mar 8, 2024 · f0ad5cd · f0ad5cd
2 parents e52143a + c27b24a
commit f0ad5cd
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Showing 7 changed files with 40 additions and 33 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+### Added
+
+### Changed
+
+## [1.0.0-rc.1] - 2024-03-08
 ### Added
 - Add `schema.yaml`
 - Add `template.config`
@@ -22,6 +28,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Add pipeline-Nextflow-module as submodule
 
 ### Changed
+- Changed pipeline name `pipeline-SQC-DNA` to `pipeline-generate-SQC-BAM`
 - Use defaults for `CollectWgsMetrics` parameters
 - Pipeline name in output dir changed to `generate-SQC-BAM`
 - Changed `remove_duplicates` option to `samtools_remove_duplicates`

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# SQC-BAM
+# generate-SQC-BAM
 
   1. [Overview](#overview)
   2. [How To Run](#how-to-run)
@@ -163,15 +163,15 @@ base_resource_update {
 
 ## Discussions
 
-- [Issue Tracker](https://github.com/uclahs-cds/pipeline-SQC-DNA/issues) to report errors and enhancement ideas.
-- Discussions can take place in [generate-SQC-BAM Discussions](https://github.com/uclahs-cds/pipeline-SQC-DNA/discussions)
-- [generate-SQC-BAM Pull Requests](https://github.com/uclahs-cds/pipeline-SQC-DNA/pulls) are also open for discussion
+- [Issue Tracker](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/issues) to report errors and enhancement ideas.
+- Discussions can take place in [generate-SQC-BAM Discussions](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/discussions)
+- [generate-SQC-BAM Pull Requests](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/pulls) are also open for discussion
 
 ---
 
 ## Contributors
 
-Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-SQC-DNA/graphs/contributors) at GitHub.
+Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/graphs/contributors) at GitHub.
 
 ---
 

diff --git a/metadata.yaml b/metadata.yaml
@@ -1,6 +1,6 @@
 ---
 category: "pipeline"
-description: "Quality control analyses for sample level data"
+description: "Sample level Quality Control analyses for BAM files"
 maintainers: "Boutros Lab Infrastructure <[email protected]>"
 languages: ["Nextflow", "Docker"]
 dependencies: ["Java", "Nextflow", "Docker"]

diff --git a/nextflow.config b/nextflow.config
@@ -3,5 +3,5 @@ manifest {
     name = 'generate-SQC-BAM'
     author = 'Sorel Fitz-Gibbon'
     description = 'Sample level QC for DNA sequencing data'
-    version = '0.0.1'
+    version = '1.0.0-rc.1'
 }
diff --git a/nftest.yml b/nftest.yml
@@ -15,22 +15,22 @@ cases:
     verbose: true
     asserts:
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
         method: md5
   - name: a_mini-all-tools-multiple-samples
     message: test all tools with 1 normal and 2 tumor samples
@@ -41,31 +41,31 @@ cases:
     verbose: true
     asserts:
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5.n1_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5.n1_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5.n1_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
         method: md5
   - name: a_mini-stats
     message: test samtools stats
@@ -76,10 +76,10 @@ cases:
     verbose: true
     asserts:
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_HG002.N_stats.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.18_TWGSAMIN_S2-v1.1.5_stats.txt
         method: md5
   - name: a_mini-collectwgsmetrics
     message: test collectwgsmetrics
@@ -90,10 +90,10 @@ cases:
     verbose: true
     asserts:
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
         script: test/assert_txt.sh
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
         script: test/assert_txt.sh
   - name: a_mini-bamqc
     message: test bamqc
@@ -104,8 +104,8 @@ cases:
     verbose: true
     asserts:
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
         method: md5
       - actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
-        expect: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
+        expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
         method: md5
diff --git a/test/yaml/a_mini-multiple-samples.yaml b/test/yaml/a_mini-multiple-samples.yaml
@@ -3,11 +3,11 @@ patient_id: 'TWGSAMIN000001'
 dataset_id: 'TWGSAMIN'
 input:
   normal:
-    - path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/HG002.N-n2.bam
+    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
       read_length: 150
 
   tumor:
-    - path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n2.bam
+    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
       read_length: 150
-    - path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
+    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
       read_length: 150
diff --git a/test/yaml/a_mini.yaml b/test/yaml/a_mini.yaml
@@ -3,9 +3,9 @@ patient_id: 'TWGSAMIN000001'
 dataset_id: 'TWGSAMIN'
 input:
   normal:
-    - path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/HG002.N-n2.bam
+    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
       read_length: 150
 
   tumor:
-    - path: /hot/software/pipeline/pipeline-SQC-DNA/Nextflow/development/test-input/S2.T-n2.bam
+    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
       read_length: 150