Align-DNA 10.0.0-rc.1 (#161)

* Update align-DNA to v10.0.0-rc.1 * Update CHANGELOG * Add align-DNa to validation * Remove redundant aligner param
uclahs-cds · Jan 31, 2024 · 46ed576 · 46ed576
1 parent f4f9761
commit 46ed576
Show file tree

Hide file tree

Showing 4 changed files with 3 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 ### Changed
 + Convert-BAM2FASTQ: 2.0.0-rc.1 -> 2.0.0-rc.2
++ Align-DNA: 9.0.0 -> 10.0.0-rc.1
 
 ---
 

diff --git a/config/methods.config b/config/methods.config
@@ -341,6 +341,7 @@ methods {
 
     validate_pipelines = {
         pipeline_param_exclusion = [
+            'pipeline-align-DNA': ['dataset_id', 'patient_id', 'sample_id', 'output_dir', 'work_dir', 'spark_temp_dir', 'input', 'input_csv'],
             'pipeline-recalibrate-BAM': ['dataset_id', 'patient_id', 'output_dir', 'input'],
             'pipeline-call-gSNP': ['dataset_id', 'patient_id', 'output_dir', 'input'],
             'pipeline-call-sSNV': ['dataset_id', 'patient_id', 'sample_id', 'output_dir', 'work_dir', 'input'],

diff --git a/external/pipeline-align-DNA b/external/pipeline-align-DNA
diff --git a/module/align_DNA/call_align_DNA.nf b/module/align_DNA/call_align_DNA.nf
@@ -26,8 +26,6 @@ process call_align_DNA {
     output_directory = "align-DNA-*/${sample}"
     bam = "align-DNA-*/${sample}/BWA-MEM2-2.2.1/output/BWA-MEM2-*${sample}.bam"
 
-    aligner = params.align_DNA.aligner.join(',')
-
     String params_to_dump = combine_input_with_params(params.align_DNA.metapipeline_arg_map)
     """
     set -euo pipefail
@@ -40,7 +38,6 @@ process call_align_DNA {
         ${moduleDir}/../../external/pipeline-align-DNA/main.nf \
         -params-file combined_align_dna_params.yaml \
         --sample_id ${sample} \
-        --aligner ${aligner} \
         --output_dir \$(pwd) \
         --work_dir \$WORK_DIR \
         --spark_temp_dir \$WORK_DIR \
+4 −4		.github/PULL_REQUEST_TEMPLATE.md
+6 −0		.github/dependabot.yml
+20 −0		.github/workflows/PlantUML.yaml
+17 −2		CHANGELOG.md
+3 −2		README.md
+21 −1		config/F16.config
+22 −2		config/F32.config
+21 −1		config/F72.config
+61 −0		config/custom_schema_types.config
+10 −4		config/default.config
+52 −139		config/methods.config
+137 −0		config/schema.yaml
+4 −0		config/template.config
+1 −1		external/nextflow-config
+1 −1		external/nextflow-modules
+12 −0		input/align-DNA.input.yaml
+15 −16		main.nf
+2 −2		metadata.yaml
+40 −31		module/align_DNA_BWA_MEM2.nf
+36 −30		module/align_DNA_HISAT2.nf
+2 −2		module/mark_duplicate_picardtools.nf
+0 −23		module/validation.nf
+1 −1		nextflow.config
+27 −0		nftest.yml
+1 −1		script/write_dna_align_config_file.py
+45 −0		test/a_mini_n2-picard.config
+44 −0		test/a_mini_n2-picard_yaml.config
+12 −0		test/a_mini_n2-picard_yaml.yaml
+45 −0		test/a_mini_n2-spark.config
+0 −0		test/archive/compareBams.nf
+0 −0		test/archive/config/compareBams.config
+0 −0		test/archive/inputs/compareBams.inputs.csv
+9 −0		test/global.config