uclahs-cds · yashpatel6 · Oct 28, 2023 · Oct 20, 2023 · Oct 21, 2023 · Oct 21, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,8 +8,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [5.0.0] - 2023-10-25
 ### Changed
 + Use data structure in params to pass outputs between pipelines
++ Update tests
++ Update README with current status and parameters
 
 ---
 

diff --git a/README.md b/README.md
@@ -7,15 +7,18 @@
   - [Pipeline Steps](#pipeline-steps)
     - [1. convert-BAM2FASTQ](#1-convert-bam2fastq)
     - [2. align-DNA](#2-align-dna)
-    - [3. call-gSNP](#3-call-gsnp)
-    - [4. call-sSNV](#4-call-ssnv)
-    - [5. call-mtSNV](#5-call-mtsnv)
-    - [6. call-gSV](#6-call-gsv)
-    - [7. call-sSV](#7-call-ssv)
+    - [3. recalibrate-BAM]($3-recalibrate-bam)
+    - [4. call-gSNP](#4-call-gsnp)
+    - [5. call-sSNV](#5-call-ssnv)
+    - [6. call-mtSNV](#6-call-mtsnv)
+    - [7. call-gSV](#7-call-gsv)
+    - [8. call-sSV](#8-call-ssv)
+    - [Sample modes](#sample-modes)
   - [Inputs](#inputs)
     - [Input BAM](#input-bam)
     - [Input FASTQ](#input-fastq)
     - [Config Params](#config-params)
+      - [UCLAHS-CDS WGS Params](#uclahs-cds-wgs-global-sample-job-submission-parameters)
   - [Outputs](#outputs)
   - [Discussions](#discussions)
   - [Contributors](#contributors)
@@ -61,27 +64,58 @@ Aligned BAM file for each sample is first converted back to FASTQ using [pipelin
 
 The FASTQ file for each sample is then realigned to the genome using [pipeline-align-DNA](https://github.com/uclahs-cds/pipeline-align-DNA).
 
-### 3. call-gSNP
+### 3. recalibrate-BAM
 
-Germline SNPs are then called from the re-aligned BAM files using [pipeline-call-gSNP](https://github.com/uclahs-cds/pipeline-call-gSNP). Call-gSNP also performs BAM re-calibration. Tumor and normal samples from the same patient are paired in this step.
+The aligned BAM goes through Indel Realignment and base quality score recalibration using [pipeline-recalibrate-BAM](https://github.com/uclahs-cds/pipeline-recalibrate-BAM).
 
-### 4. call-sSNV
+### 4. call-gSNP
 
-The calibrated BAM from step 3 is then used to call for somatic SNVs using [pipeline-call-sSNV](https://github.com/uclahs-cds/pipeline-call-sSNV).
+Germline SNPs are then called from the re-calibrated BAMs using [pipeline-call-gSNP](https://github.com/uclahs-cds/pipeline-call-gSNP).
 
-### 5. call-mtSNV
+### 5. call-sSNV
 
-The same calibrated BAM from step 3 is also used to call for mitochondrial SNVs usint [pipeline-call-mtSNV](https://github.com/uclahs-cds/pipeline-call-mtSNV)
+The re-calibrated BAMs from step 3 are then used to call somatic SNVs using [pipeline-call-sSNV](https://github.com/uclahs-cds/pipeline-call-sSNV).
 
-### 6. call-gSV
+### 6. call-mtSNV
 
-The same recalibrated BAM from step 3 is also used to call for germline structural variants using [pipeline-call-gSV](https://github.com/uclahs-cds/pipeline-call-gSV)
+The re-calibrated BAMs from step 3 are used to call mitochondrial SNVs using [pipeline-call-mtSNV](https://github.com/uclahs-cds/pipeline-call-mtSNV).
+
+### 7. call-gSV
+
+The re-calibrated BAMs from step 3 are used to call germline structural variants using [pipeline-call-gSV](https://github.com/uclahs-cds/pipeline-call-gSV).
 
 > **Note**: The `run_regenotyping` mode from the call-gSV pipeline is disabled for the metapipeline. Regenotyping should be performed separately at the cohort-level.
 
-### 7. call-sSV
+### 8. call-sSV
+
+The re-calibrated BAMs from step 3 are used to call for somatic structural variants using [pipeline-call-sSV](https://github.com/uclahs-cds/pipeline-call-sSV).
+
+### Sample modes
+
+The metapipeline supports running samples in three modes: `single`, `paired`, and `multi`.
+
+#### Single sample mode
+All samples are processed individually as separate jobs.
+- Normal samples will go through germline calling (call-gSNP, call-gSV) and somatic SNV calling with Mutect2's normal-only mode.
+- Tumor samples will go through germline calling (call-gSNP) and somatic SNV calling with Mutect2's tumor-only mode.
+
+#### Paired sample mode
 
-The same recalibrated BAM(s) from step 3 are also used to call for somatic structural variants using [pipeline-call-sSV](https://github.com/uclahs-cds/pipeline-call-sSV)
+All samples from the same patient are processed as a single job.
+- Individual samples will go through the convert-BAM2FASTQ and align-DNA pipelines.
+- The normal sample will then be paired with each tumor sample and each pair will go through recalibrate-BAM, call-gSNP, call-sSNV, call-mtSNV, and call-sSV.
+- The normal sample will go through call-gSV.
+
+#### Multi sample mode
+
+All samples from the same patient are processed as a single job.
+- Individual samples will go through the convert-BAM2FASTQ and align-DNA pipelines.
+- The recalibration and germline SNP calling will then proceed on the entire set of samples together.
+- Somatic SNV calling will proceed in two ways:
+    1. The normal sample will be paired with each tumor sample and run through the call-sSNV pipeline
+    2. If Mutect2 was requested, the entire set of samples will go through multi-sample calling with just Mutect2 in call-sSNV.
+- The normal sample will be paired with each tumor sample and each pair will go through call-mtSNV and call-sSV.
+- The normal sample will go through call-gSV.
 
 ---
 
@@ -124,17 +158,30 @@ See this [template](input/template-input-FASTQ.csv) for CSV format and this [tem
 | Input Parameter | Type | Required | Description |
 | :---: | :--: | :------: | :---------: |
 | `input_csv` | path | no | Absolute path to input CSV when using CSV input format |
- `output_dir` | path | yes | Absolute path to directory where output files will be saved |
+| `output_dir` | path | yes | Absolute path to directory where output files will be saved |
 | `leading_work_dir` | path | yes | Absolute path to **common** working directory (under `/hot` for example for access across all nodes). **Cannot** be `/scratch` |
 | `pipeline_work_dir` | path | yes | Absolute path to outputs from each individual pipeline before copying to `output_dir`. Default: `/scratch` |
 | `project_id` | string | yes | Project identifier |
 | `save_intermediate_files` | boolean | yes | Whether to save intermediate files. Default: `false` |
 | `partition` | string | yes | Partition type for submitting each processing jobs |
 | `clusterOptions` | string | yes | Additional `slurm` submission options |
-| `per_job_cpus` | integer | yes | Number of CPUs per job |
-| `per_job_memory` | float | yes | Memory requested per job |
 | `max_parallel_jobs` | integer | yes | Number of jobs to submit at once. Default:  5 |
+| `cluster_submission_interval` | integer | yes | Time in minutes to wait between job submissions, Default: 90 |
 | `sample_mode` | string | yes | Mode for sample calling. Options: `paired`, `single`, `multi`. Default: `paired` |
+| `requested_pipelines` | list | yes | List of pipelines requested. |
+| `override_realignment` | boolean | yes | Whether to override conversion to FASTQ and realignment when given BAM input. Default: `false` |
+| `override_recalibrate_bam` | boolean | yes | Whether to override recalibrate-BAM pipeline when given BAM input. Default: `false` |
+
+#### UCLAHS-CDS WGS global sample job submission parameters
+
+The following parameters are intended to control the global number and rate of WGS jobs. By default, these parameters are enabled; in the case of non-WGS samples, disable `uclahs_cds_wgs` in the config file params.
+
+| Input Parameter | Type | Required | Description |
+| :---: | :--: | :------: | :---------: |
+| `uclahs_cds_wgs` | boolean | yes | Whether global job number and submission limits should be applied. Default: `true` |
+| `global_allowed_jobs` | integer | yes | Global number of WGS jobs allowed. Default: 12 |
+| `per_user_allowed_jobs` | integer | yes | Number of jobs allowed to be running per-user. Default: 3 |
+| `global_rate_limit` | integer | yes | Time in minutes between submission of any WGS jobs. Default: 90 |
 
 ---
 
@@ -164,7 +211,7 @@ metapipeline-DNA is licensed under the GNU General Public License version 2. See
 
 metapipeline-DNA performs alignment, germline SNP calling, somatic SNV calling, and mitochondrial SNV calling for given samples.
 
-Copyright (C) 2021-2022 University of California Los Angeles ("Boutros Lab") All rights reserved.
+Copyright (C) 2021-2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
 
 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
 

diff --git a/external/pipeline-recalibrate-BAM b/external/pipeline-recalibrate-BAM
diff --git a/module/align_DNA/create_CSV_align_DNA.nf b/module/align_DNA/create_CSV_align_DNA.nf
@@ -18,7 +18,7 @@ process create_CSV_align_DNA {
     publishDir path: "${params.log_output_dir}/process-log",
         mode: "copy",
         pattern: ".command.*",
-        saveAs: { "${task.process}-${params.patient}/${sample}/log${file(it).getName()}" }
+        saveAs: { "${task.process.replace(':', '/')}-${params.patient}/${sample}/log${file(it).getName()}" }
 
     publishDir path: "${params.output_dir}/intermediate/${task.process}-${params.patient}/${sample}",
         enabled: params.save_intermediate_files,

diff --git a/module/call_gSNP/default.config b/module/call_gSNP/default.config
@@ -49,3 +49,9 @@ params {
 
 // Setup the pipeline config. DO NOT REMOVE THIS LINE!
 methods.setup()
+
+if (docker.containsKey('runOptions') && docker.runOptions) {
+    docker.runOptions = "${docker.runOptions}" + " -v ${params.work_dir}:${params.work_dir}"
+} else {
+    docker.runOptions = " -v ${params.work_dir}:${params.work_dir}"
+}
diff --git a/module/call_gSNP/workflow.nf b/module/call_gSNP/workflow.nf
@@ -55,11 +55,7 @@ workflow call_gSNP {
             input_ch_normal.mix(input_ch_tumor).set{ input_ch_create_call_gsnp_yaml }
         }
 
-        input_ch_create_call_gsnp_yaml.view{ "INPUT_CREATE: ${it}" }
-
         create_YAML_call_gSNP(input_ch_create_call_gsnp_yaml)
 
-        create_YAML_call_gSNP.out.call_gsnp_input.view{ "INPUT_GSNP: ${it}" }
-
         run_call_gSNP(create_YAML_call_gSNP.out.call_gsnp_input)
 }
diff --git a/module/convert_BAM2FASTQ/identify_outputs.nf b/module/convert_BAM2FASTQ/identify_outputs.nf
@@ -5,7 +5,7 @@ workflow identify_convert_bam2fastq_outputs {
     och_convert_BAM2FASTQ
 
     main:
-    och_convert_BAM2FASTQ.view().map{ bam2fastq_out ->
+    och_convert_BAM2FASTQ.map{ bam2fastq_out ->
         new File(bam2fastq_out[3].toRealPath().toString()).eachLine{ line, line_num ->
             if (line_num == 1) { return; };
             def rg_info = line.split(",");

diff --git a/nextflow.config b/nextflow.config
@@ -3,5 +3,5 @@ manifest {
     name = 'metapipeline-DNA'
     author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Mohammed Faizal Eeman Mootor']
     description = 'Nextflow pipeline to convert BAM to FASTQ, align, call gSNP, call sSNV, call gSV, call sSV and call mtSNV'
-    version = '5.0.0-rc.10'
+    version = '5.0.0'
 }
diff --git a/nftest.yaml b/nftest.yaml
@@ -21,11 +21,6 @@ cases:
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/output/TCEB1/TCEB1_RCC_S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R2.fq.gz
         script: test/test-bam2fastq/assert_fastq.sh
 
-      - actual: intermediate/convert_BAM2FASTQ/create_CSV_align_DNA-TCEB1/TCEB1_RCC_S00-9422N_079_114/align_DNA_input.csv
-        expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/output/TCEB1/align_DNA_input.csv
-        script: test/test-bam2fastq/assert_input_csv.py
-
-
   - name: test-align-DNA
     message: Test align-DNA
     nf_script: test/test-align-DNA/test.nf
@@ -56,8 +51,8 @@ cases:
     verbose: true
     skip: true
     asserts:
-      - actual: output/call-gSNP-10.0.0-rc.1/9422/GATK-4.2.4.1/output/GATK-4.2.4.1_test_S00-9422T-027-166.g.vcf.gz
-        expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/output/test-call-gSNP/TCEB1/S00-9422T_027_166_merged_raw_variants.g.vcf.gz
+      - actual: output/call-gSNP-10.0.0-rc.3/9422T/GATK-4.2.4.1/output/GATK-4.2.4.1_test_S00-9422T-027-166.g.vcf.gz
+        expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/output/test-call-gSNP/TCEB1/GATK-4.2.4.1_test_S00-9422T-027-166.g.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
 
   #   Disabling BAM comparison for now - checksums differ even if tools like GATK CompareSAMs report identical BAM files
@@ -73,40 +68,40 @@ cases:
     verbose: true
     skip: true
     asserts:
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-concat.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-concat.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/BCFtools-1.17_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-concat.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/MuSE-2.0.2/output/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/MuSE-2.0.3/output/MuSE-2.0.3_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_MNV.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_MNV.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_MNV.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
-      - actual: output/call-sSNV-7.0.0-rc.1/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
+      - actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
         script: test/test-call-gSNP/assert_vcf.sh
 

diff --git a/test/test-align-DNA/input.csv b/test/test-align-DNA/input.csv
+1 −1		.github/workflows/cicd-base.yaml
+7 −0		CHANGELOG.md
+5 −5		config/custom_schema_types.config
+3 −2		main.nf
+1 −1		nextflow.config