Add method to dump params object

[j2salmingo]

Description

Adds the method to dump the params object to the log directory.

Testing Results

NFTest

input:
sample_id: a_mini_n2_spark
input_csv: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv
reference_fasta_bwa: /hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa
reference_fasta_index_files_bwa: /hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa.*
reference_fasta_hisat2: /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta
reference_fasta_index_files_hisat2: /hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38.*.ht2

output:
work_dir: /scratch/203433
output_dir: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark
output_dir_base_bwa: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark
output_dir_base_hisat2: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark
log_output_dir_bwa: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark/log-align-DNA-10.1.0-20240805T185700Z/
log_output_dir_hisat2: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark/log-align-DNA-10.1.0-20240805T185700Z/

Checklist

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have reviewed the Nextflow pipeline standards.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up the branch protection rule following the github standards before opening this pull request, or the branch protection rule has already been set up.

• I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample with aligner setting to BWA-MEM2, HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.

[kiarod]

Looks good! params.json seems to be created properly.

{
    "max_cpus": 32,
    "max_memory": {
        "mega": 62240,
        "kilo": 63733760,
        "giga": 60,
        "bytes": 65263370240
    },
    "min_cpus": 1,
    "min_memory": {
        "mega": 1,
        "kilo": 1024,
        "giga": 0,
        "bytes": 1048576
    },
    "ucla_cds": true,
    "mark_duplicates": true,
    "gatk_command_mem_diff": {
        "mega": 5120,
        "kilo": 5242880,
        "giga": 5,
        "bytes": 5368709120
    },
    "bwa_version": "BWA-MEM2-2.2.1",
    "hisat2_version": "HISAT2-2.2.1",
    "docker_container_registry": "ghcr.io/uclahs-cds",
    "pipeval_version": "4.0.0-rc.2",
    "bwa_and_samtools_version": "2.2.1_samtools-1.17",
    "hisat2_and_samtools_version": "2.2.1_samtools-1.17",
    "picardtools_version": "3.1.1",
    "output_dir": "/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark",
    "docker_image_bwa_and_samtools": "ghcr.io/uclahs-cds/bwa-mem2:2.2.1_samtools-1.17",
    "docker_image_hisat2_and_samtools": "ghcr.io/uclahs-cds/hisat2:2.2.1_samtools-1.17",
    "docker_image_picardtools": "ghcr.io/uclahs-cds/picard:3.1.1",
    "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
    "docker_image_gatk": "broadinstitute/gatk:4.2.4.1",
    "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.17",
    "ucla_cds_analyte": "DNA",
    "sample_id": "a_mini_n2_spark",
    "input_csv": "/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv",
    "dataset_id": "0000000",
    "reference_fasta_bwa": "/hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa",
    "reference_fasta_hisat2": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
    "hisat2_index_prefix": "/hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38",
    "aligner": [
        "BWA-MEM2",
        "HISAT2"
    ],
    "save_intermediate_files": false,
    "cache_intermediate_pipeline_steps": false,
    "enable_spark": true,
    "spark_metrics": false,
    "ucla_cds_registered_dataset_input": false,
    "ucla_cds_registered_dataset_output": false,
    "input": {
        "FASTQ": [
            {
                "read_group_identifier": "HG002.N.seq1",
                "sequencing_center": "BS",
                "library_identifier": "bamsurgeon",
                "platform_technology": "ILLUMINA",
                "platform_unit": "NA",
                "lane": "1",
                "sample": "HG002.N",
                "read1_fastq": "/hot/data/TEST/TEST0000000/TWGSAMIN000001/TWGSAMIN000001-N001-S01-F/DNA/WGS/raw/FASTQ/HG002-N-A-mini-n2/HG002.N-n2_R1.fq.gz",
                "read2_fastq": "/hot/data/TEST/TEST0000000/TWGSAMIN000001/TWGSAMIN000001-N001-S01-F/DNA/WGS/raw/FASTQ/HG002-N-A-mini-n2/HG002.N-n2_R2.fq.gz"
            }
        ]
    },
    "make_duplicates": true,
    "disable_alt_aware": false,
    "ucla_cds_registed_dataset_output": false,
    "output_dir_base": "/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark",
    "log_output_dir": "/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-add-param-dump/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark/log-align-DNA-10.1.0-20240805T185700Z/",
    "work_dir": "/scratch/203433",
    "spark_temp_dir": "/scratch/203433",
    "reference_fasta_index_files_bwa": "/hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa.*",
    "reference_fasta_index_files_hisat2": "/hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38.*.ht2"
}

[kiarod]

whoops sorry @j2salmingo didn't mean to merge it in myself just went into autopilot