Release v1.0.0 (#58)

* Bump version in CHANGELOG * Bump version in nextflow.config * Update test paths * Update expected changes in tests --------- Co-authored-by: Nicholas Wiltsie <[email protected]>
uclahs-cds · Mar 13, 2024 · 2040581 · 2040581
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [1.0.0] - 2024-03-13
 ### [Added]
 - Sort BAMs before merging for consistent order of output BAM @PG header lines
 - Add NFTest case

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 // Metadata
 manifest {
     name = 'recalibrate-BAM'
-    author = 'Yash Patel'
+    author = 'Yash Patel, Nicholas Wiltsie'
     description = 'Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration'
-    version = '1.0.0-rc.4'
+    version = '1.0.0'
 }
diff --git a/nftest.yml b/nftest.yml
@@ -12,15 +12,15 @@ cases:
     skip: false
     verbose: true
     asserts:
-      - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam
+      - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam
         expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam
         method: md5
-      - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai
+      - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.bai
         expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai
         method: md5
-      - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512
+      - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.sha512
         expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512
         method: md5
-      - actual: recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512
+      - actual: recalibrate-BAM-*/TWGSAMIN000001/GATK-*/output/BWA-MEM2-*_GATK-*_A-mini_S2-v1.1.5.bam.bai.sha512
         expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512
         method: md5
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -36,10 +36,10 @@
       "uid_and_gid": "-u $(id -u):$(id -g)"
     },
     "manifest": {
-      "author": "Yash Patel",
+      "author": "Yash Patel, Nicholas Wiltsie",
       "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration",
       "name": "recalibrate-BAM",
-      "version": "1.0.0-rc.4"
+      "version": "1.0.0"
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
@@ -74,7 +74,7 @@
       "is_DOC_run": false,
       "is_emit_original_quals": true,
       "is_targeted": false,
-      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z",
+      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z",
       "max_cpus": "16",
       "max_memory": "31 GB",
       "metapipeline_delete_input_bams": false,
@@ -85,7 +85,7 @@
       "min_cpus": "1",
       "min_memory": "1 MB",
       "output_dir": "/tmp/outputs",
-      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1",
+      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
@@ -414,15 +414,15 @@
     },
     "report": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/report.html"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html"
     },
     "timeline": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/timeline.html"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html"
     },
     "trace": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/trace.txt"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt"
     },
     "workDir": "/scratch/851543"
   }

diff --git a/test/configtest-F32.json b/test/configtest-F32.json
@@ -36,10 +36,10 @@
       "uid_and_gid": "-u $(id -u):$(id -g)"
     },
     "manifest": {
-      "author": "Yash Patel",
+      "author": "Yash Patel, Nicholas Wiltsie",
       "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration",
       "name": "recalibrate-BAM",
-      "version": "1.0.0-rc.4"
+      "version": "1.0.0"
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
@@ -74,7 +74,7 @@
       "is_DOC_run": false,
       "is_emit_original_quals": true,
       "is_targeted": false,
-      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z",
+      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z",
       "max_cpus": "32",
       "max_memory": "64 GB",
       "metapipeline_delete_input_bams": false,
@@ -85,7 +85,7 @@
       "min_cpus": "1",
       "min_memory": "1 MB",
       "output_dir": "/tmp/outputs",
-      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1",
+      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
@@ -414,15 +414,15 @@
     },
     "report": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/report.html"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html"
     },
     "timeline": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/timeline.html"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html"
     },
     "trace": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-19970704T165655Z/nextflow-log/trace.txt"
+      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt"
     },
     "workDir": "/scratch/851543"
   }