Add a proper intro to IDE features

mkdocs.yml

@@ -48,6 +48,7 @@ nav:
   - Side Quests:
       - side_quests/index.md
       - side_quests/orientation.md
+      - side_quests/ide_features.md
       - side_quests/workflows_of_workflows.md
       - side_quests/splitting_and_grouping.md
       - side_quests/nf-test.md

side-quests/ide_features/basic_workflow.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+include { FASTQC } from './modules/fastqc.nf'
+
+/*
+ * Workflow parameters
+ */
+params.input = 'data/sample_data.csv'
+params.output_dir = 'results'
+
+/*
+ * Main workflow demonstrating module usage and navigation
+ */
+workflow {
+    // Create input channel from CSV file
+    ch_input = Channel.fromPath(params.input, checkIfExists: true)
+        .splitCsv(header: true)
+        .map { row ->
+            return [row.sample_id, file(row.fastq_path)]
+        }
+        .view { "Processing sample: ${it[0]} -> ${it[1]}" }
+
+    // Run FastQC process - Ctrl-click on FASTQC to navigate to module
+    FASTQC(ch_input)
+
+    // View outputs
+    FASTQC.out.html.view { "FastQC report: ${it}" }
+    FASTQC.out.zip.view { "FastQC data: ${it}" }
+}

side-quests/ide_features/complex_workflow.nf

@@ -0,0 +1,88 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Complex Workflow Example for IDE Navigation Training
+ */
+
+include { FASTQC } from './modules/fastqc'
+include { STAR_ALIGN } from './modules/star'
+include { MULTIQC } from './modules/utils'
+
+process TRIM_GALORE {
+    tag "${sample_id}"
+    publishDir "${params.output}/trimmed", mode: 'copy'
+
+    input:
+    tuple val(sample_id), path(reads)
+
+    output:
+    tuple val(sample_id), path("${sample_id}_trimmed_*.fq.gz")
+
+    script:
+    """
+    trim_galore --paired ${reads}
+    """
+}
+
+process FEATURECOUNTS {
+    tag "${sample_id}"
+    publishDir "${params.output}/counts", mode: 'copy'
+
+    input:
+    tuple val(sample_id), path(bam), path(gtf)
+
+    output:
+    tuple val(sample_id), path("${sample_id}_counts.txt")
+
+    script:
+    """
+    featureCounts -p -t exon -g gene_id -a ${gtf} -o ${sample_id}_counts.txt ${bam}
+    """
+}
+
+workflow RNASEQ_PIPELINE {
+    take:
+    reads_ch
+    reference_ch
+    gtf_ch
+
+    main:
+    // Quality control
+    FASTQC(reads_ch)
+
+    // Trimming
+    TRIM_GALORE(reads_ch)
+
+    // Alignment
+    STAR_ALIGN(TRIM_GALORE.out, reference_ch)
+
+    // Quantification
+    count_input = STAR_ALIGN.out.combine(gtf_ch)
+    FEATURECOUNTS(count_input)
+
+    // Aggregate QC
+    qc_files = FASTQC.out.mix(TRIM_GALORE.out)
+    MULTIQC(qc_files.collect())
+
+    emit:
+    counts = FEATURECOUNTS.out
+    qc_report = MULTIQC.out
+}
+
+workflow {
+    // Input channels
+    ch_read = Channel.fromPath(params.input)
+        .splitCsv(header: true)
+        .map { row -> [row.sample_id, [file(row.fastq_1), file(row.fastq_2)]] }
+
+    ch_reference = Channel.fromPath(params.reference)
+    ch_gtf = Channel.fromPath(params.gtf)
+
+    // Execute pipeline
+    RNASEQ_PIPELINE(ch_reads, ch_reference, ch_gtf)
+
+    // Output summary
+    RNASEQ_PIPELINE.out.counts
+        .collectFile(name: 'expression_matrix.txt', sort: true)
+        .view { "Expression matrix created: ${it}" }
+}

side-quests/ide_features/data/sample_data.csv

@@ -0,0 +1,6 @@
+sample_id,fastq_path
+sample_001,data/sample_001.fastq.gz
+sample_002,data/sample_002.fastq.gz
+sample_003,data/sample_003.fastq.gz
+sample_004,data/sample_004.fastq.gz
+sample_005,data/sample_005.fastq.gz

side-quests/ide_features/modules/fastqc.nf

@@ -0,0 +1,26 @@
+process FASTQC {
+    tag "${sample_id}"
+    publishDir "${params.output_dir}/fastqc", mode: 'copy'
+
+    // Container directive for reproducibility
+    container 'biocontainers/fastqc:v0.11.9_cv8'
+
+    input:
+    tuple val(sample_id), path(reads)
+
+    output:
+    tuple val(sample_id), path("*.html"), emit: html
+    tuple val(sample_id), path("*.zip"), emit: zip
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    fastqc \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        ${reads}
+    """
+}

side-quests/ide_features/modules/star.nf

@@ -0,0 +1,32 @@
+process STAR_ALIGN {
+    tag "${sample_id}"
+    publishDir "${params.output}/alignments", mode: 'copy'
+    container 'biocontainers/star:2.7.10a_cv1'
+    cpus 8
+    memory '32.GB'
+
+    input:
+    tuple val(sample_id), path(reads)
+    path reference_dir
+
+    output:
+    tuple val(sample_id), path("${sample_id}_Aligned.sortedByCoord.out.bam")
+
+    script:
+    """
+    STAR \\
+        --runThreadN ${task.cpus} \\
+        --genomeDir ${reference_dir} \\
+        --readFilesIn ${reads} \\
+        --readFilesCommand zcat \\
+        --outFileNamePrefix ${sample_id}_ \\
+        --outSAMtype BAM SortedByCoordinate \\
+        --outSAMunmapped Within \\
+        --outSAMattributes Standard
+    """
+
+    stub:
+    """
+    touch ${sample_id}_Aligned.sortedByCoord.out.bam
+    """
+}

side-quests/ide_features/modules/utils.nf

@@ -0,0 +1,46 @@
+process MULTIQC {
+    publishDir "${params.output}/multiqc", mode: 'copy'
+    container 'biocontainers/multiqc:1.13_cv1'
+    cpus 2
+    memory '4.GB'
+
+    input:
+    path qc_files
+
+    output:
+    path "multiqc_report.html"
+    path "multiqc_data/"
+
+    script:
+    """
+    multiqc \\
+        --force \\
+        --title "Pipeline QC Report" \\
+        --filename multiqc_report.html \\
+        .
+    """
+
+    stub:
+    """
+    mkdir multiqc_data
+    touch multiqc_report.html
+    """
+}
+
+process CUSTOM_DUMPSOFTWAREVERSIONS {
+    publishDir "${params.output}/pipeline_info", mode: 'copy'
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.yml"
+    path "software_versions_mqc.yml"
+
+    script:
+    """
+    cat ${versions} > software_versions.yml
+    echo 'id: "software_versions"' > software_versions_mqc.yml
+    echo 'section_name: "Software Versions"' >> software_versions_mqc.yml
+    """
+}

side-quests/ide_features/nextflow.config

@@ -0,0 +1,6 @@
+/*
+ * Nextflow Configuration for IDE Features Training
+ */
+
+
+docker.enabled = true