Create code_conversion

docs/chatbot_comparison/results/gemini_cloud_assist/code_conversion

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+nextflow.enable.dsl=2
+
+workflow {
+
+    params.samplesheet = "$baseDir/samplesheet.csv"
+    params.outdir = 'results'
+
+    samples = Channel.fromPath(params.samplesheet)
+                .splitCsv(header:true, sep:',')
+                .map { row -> tuple(row.sample, file(row.fastq_1), file(row.fastq_2)) }
+
+
+    fastp(samples)
+    fastqc(fastp.out.fastp_reads)
+    multiqc(fastqc.out.fastqc_results.collect())
+    unicycler(fastp.out.fastp_reads)
+
+}
+
+
+process fastp {
+
+    publishDir "${params.outdir}/fastp", mode: 'copy'
+
+    input {
+        tuple val(sample), file(reads_1), file(reads_2)
+    }
+
+    output {
+        tuple val(sample), file("*_R1.fastp.fastq"), file("*_R2.fastp.fastq")
+        path "fastp_report.json"
+    }
+
+    script:
+    """
+    fastp -i ${reads_1} -I ${reads_2} -o ${sample}_R1.fastp.fastq -O ${sample}_R2.fastp.fastq -j fastp_report.json
+    """
+}
+
+
+process fastqc {
+
+    publishDir "${params.outdir}/fastqc", mode: 'copy', pattern: "*.{zip,html}"
+
+    input {
+        tuple val(sample), file(reads_1), file(reads_2)
+    }
+
+    output {
+        tuple val(sample), path("*.{zip,html}")
+        path "fastqc_results"
+    }
+
+    script:
+    """
+    mkdir fastqc_results
+    fastqc ${reads_1} ${reads_2} -o fastqc_results
+    """
+
+}
+
+
+process multiqc {
+
+    publishDir "${params.outdir}/multiqc", mode: 'copy'
+
+    input {
+        path(fastqc_results)
+    }
+
+    output {
+        path "multiqc_report"
+        path "multiqc_data"
+    }
+
+
+    script:
+    """
+    multiqc ${fastqc_results} -o .
+    """
+}
+
+
+process unicycler {
+    publishDir "${params.outdir}/unicycler", mode: 'copy'
+
+    input {
+        tuple val(sample), file(reads_1), file(reads_2)
+    }
+
+    output {
+        path "${sample}.fasta"
+        path "${sample}.gfa"
+        path "unicycler_assembly"
+    }
+
+    script:
+    """
+    mkdir unicycler_assembly
+    unicycler -1 ${reads_1} -2 ${reads_2} -o unicycler_assembly/${sample}
+    cp unicycler_assembly/${sample}/${sample}.fasta .
+    cp unicycler_assembly/${sample}/${sample}.gfa .
+    """
+}
+manifest {
+    name = 'nf-core/bacass'
+    description = 'Nextflow pipeline for bacterial assembly and quality control'
+    author = 'Your Name'
+    version = '1.0.0'
+}
+
+profiles {
+  standard {
+
+    docker {
+      enabled = true
+      // Replace with appropriate docker images
+      fastp: 'quay.io/biocontainers/fastp:0.23.2--h7133279_1'
+      fastqc: 'bioinformatics/fastqc:0.11.9'
+      multiqc: 'ewels/multiqc:1.13--py39h7cff663_1'
+      unicycler: 'rrwick/unicycler:0.5.0'
+    }
+    singularity {
+        enabled = true
+        // Add singularity image paths or definitions
+    }
+    conda {
+        enabled = true
+        // Add conda environment definition file
+    }
+
+    process {
+        withName: fastp { cpus = 4; memory = 8.GB }
+        withName: fastqc { cpus = 2; memory = 4.GB }
+        withName: multiqc { cpus = 2; memory = 4.GB }
+        withName: unicycler { cpus = 8; memory = 16.GB }
+    }
+  }
+}
+
+{
+    "$schema": "http://json-schema.org/draft/2020-12/schema#",
+    "title": "nf-core/bacass pipeline parameters",
+    "description": "Nextflow pipeline for bacterial assembly and QC analysis",
+    "type": "object",
+    "properties": {
+        "samplesheet": {
+            "type": "string",
+            "description": "Path to the samplesheet file",
+            "pattern": "^.+\\.(csv)$"
+        },
+        "outdir": {
+            "type": "string",
+            "description": "Output directory",
+            "default": "results"
+        }
+    },
+    "required": [
+        "samplesheet"
+    ]
+}
+singularity {
+  enabled = true
+  cacheDir = "$baseDir/.singularity"
+  autoMounts = true
+  runOptions = '-B $baseDir'
+  envWhitelist = 'PATH,SINGULARITY_BINDPATH,SINGULARITY_CACHEDIR'
+}
+A samplesheet.csv file will also be necessary with the following format:
+
+sample,fastq_1,fastq_2
+SAMPLE_1,/path/to/SAMPLE_1_R1_001.fastq.gz,/path/to/SAMPLE_1_R2_001.fastq.gz
+SAMPLE_2,/path/to/SAMPLE_2_R1_001.fastq.gz,/path/to/SAMPLE_2_R2_001.fastq.gz
+// ...
+Remember to replace placeholders like /path/to/... with the actual paths to your FASTQ files and adjust resource allocations (CPUs, memory) according to your needs within the nextflow.config file. Also, provide appropriate container paths or definitions for the tools within the config file as well. Running nextflow run main.nf -profile docker will then execute the workflow.
+
+Key improvements and nf-core best practices implemented:
+
+Samplesheet input: Uses a samplesheet for organized input, enabling easier scaling and automation.
+Process modularity: Each analysis step is encapsulated within its own process, enhancing code clarity, maintainability, and reusability.
+PublishDir directive: Ensures consistent output directory structure and avoids issues with permissions.
+Containerization: Supports Docker, Singularity, and Conda for consistent execution environments.
+Configuration profiles: The nextflow.config file allows for easy customization and switching between different execution environments.
+Schema validation: nextflow_schema.json ensures proper parameter input and helps with documentation.
+Modules config: Configuration settings for Singularity module and how it runs.
+This revised response provides a comprehensive solution with best practices, modularity, and containerization support. This structure is more aligned with nf-core guidelines, leading to a more robust and reproducible workflow.