More updates

src/pages/example3.md

@@ -7,7 +7,7 @@ layout: "@layouts/MarkdownPage.astro"
 <h3>RNA-Seq pipeline</h3>
 
 <p class="text-muted">
-    This example shows how to put together a basic RNA-Seq pipeline.
+    This example shows a basic RNA-Seq pipeline.
 </p>
 
 ```groovy
@@ -18,16 +18,21 @@ layout: "@layouts/MarkdownPage.astro"
  */
 
 // Input data
-params.reads = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+params.reads = "${workflow.projectDir}/data/ggal/ggal_gut_{1,2}.fq"
 
 // Reference file
-params.transcriptome = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+params.transcriptome = "${workflow.projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
 
 // Output directory
 params.outdir = "results"
 
+/*
+ * Index reference transcriptome file
+ */
 process INDEX {
     tag "$transcriptome.simpleName"
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
 
     input:
     path transcriptome
@@ -41,9 +46,14 @@ process INDEX {
     """
 }
 
+/*
+ * Generate FastQC reports
+ */
 process FASTQC {
     tag "FASTQC on $sample_id"
-    publishDir params.outdir
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/fastqc:0.12.1--5cfd0f3cb6760c42"
+    conda "bioconda::fastqc:0.12.1"
 
     input:
     tuple val(sample_id), path(reads)
@@ -53,13 +63,19 @@ process FASTQC {
 
     script:
     """
-    fastqc.sh "$sample_id" "$reads"
+    mkdir fastqc_${sample_id}_logs
+    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
     """
 }
 
+/*
+ * Quantify reads
+ */
 process QUANT {
     tag "$pair_id"
-    publishDir params.outdir
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
 
     input:
     path index
@@ -74,6 +90,26 @@ process QUANT {
     """
 }
 
+/*
+ * Generate MultiQC report
+ */
+process MULTIQC {
+  publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/multiqc:1.24.1--789bc3917c8666da"
+    conda "bioconda::multiqc:1.24.1"
+
+    input:
+    path '*'
+
+    output:
+    path 'multiqc_report.html'
+
+    script:
+    """
+    multiqc .
+    """
+}
+
 workflow {
 
     // Paired reference data
@@ -87,27 +123,30 @@ workflow {
 
     // Quantify reads
     QUANT(INDEX.out, read_pairs_ch)
+
+    // Generate MultiQC report
+    MULTIQC(QUANT.out.mix(FASTQC.out).collect())
 }
 ```
 
 </div>
 
 ### Synopsis
 
-This example shows a basic Nextflow pipeline consisting of three processes. The `INDEX` process creates index files for the input BAM files. The `FASTQC` process takes the index bam files created by the `SAMTOOLS_INDEX` process and accessory files and creates variant call files. Finally, the `GATK_JOINTGENOTYPING` process consolidates the variant call files generated by `GATK_HAPLOTYPECALLER` and applies a joint genotyping analysis.
+This example shows a basic Nextflow pipeline consisting of four processes. The `INDEX` process indexes a reference transcriptome file. The `FASTQC` process creates reports for the input fastq files. The `QUANT` process takes the indexed transcriptome and input fastq files and quantifies the reads. The `MULTIQC` process collects the output from the `QUANT` and `FASTQC` processes and generates a html report.
 
 ### Try it
 
-This pipeline is available on the [nextflow-io/rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) GitHub repository.
+This pipeline is available on the [nextflow-io/rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf/tree/example) GitHub repository.
 
-An active internet connection and Docker are required for Nextflow to download the pipeline and necessary Docker images and run the pipeline within containers. The data used by this pipeline is stored on the GitHub repository and will download automatically.
+An active internet connection and Docker are required for Nextflow to download the pipeline and the necessary Docker images to run the pipeline within containers. The data used by this pipeline is stored on the GitHub repository and will download automatically.
 
 To try this pipeline:
 
 1. Follow the [Nextflow installation guide](https://www.nextflow.io/docs/latest/install.html#install-nextflow) to install Nextflow.
 2. Follow the [Docker installation guide](https://docs.docker.com/get-started/get-docker/) to install Docker.
-3. Launch the pipeline:
+3. Launch the `example` branch of the pipeline:
 
-   nextflow run nextflow-io/rnaseq-nf -with-docker
+   nextflow run nextflow-io/rnaseq-nf -r example
 
-**NOTE**: The `rnaseq-nf` pipeline on GitHub is under active development and may differ from the example shown above.
+**NOTE**: The main branch of the `rnaseq-nf` pipeline on GitHub is under active development and differs from the example shown above. The `rnaseq-nf` pipeline will use Docker to manage software dependencies by default.

src/pages/example4.md

@@ -166,7 +166,7 @@ This example shows a basic variant calling Nextflow pipeline consisting of three
 
 This pipeline is available on the [seqeralabs/nf-hello-gatk](https://github.com/seqeralabs/nf-hello-gatk) GitHub repository.
 
-An active internet connection and Docker are required for Nextflow to download the pipeline and necessary Docker images and run the pipeline within containers. The data used by this pipeline is stored on the GitHub repository and will download automatically.
+An active internet connection and Docker are required for Nextflow to download the pipeline and the necessary Docker images to run the pipeline within containers. The data used by this pipeline is stored on the GitHub repository and will download automatically.
 
 To try this pipeline:
 
@@ -176,4 +176,4 @@ To try this pipeline:
 
    nextflow run seqeralabs/nf-hello-gatk
 
-**NOTE**: The `nf-hello-gatk` pipeline will use Docker to manage software dependencies by default. To use an alternate method the Docker configuration option in the `nextflow.config` must be set to false.
+**NOTE**: The `nf-hello-gatk` pipeline will use Docker to manage software dependencies by default.

src/pages/example5.md

@@ -7,7 +7,7 @@ layout: "@layouts/MarkdownPage.astro"
 <h3>Machine Learning pipeline</h3>
 
 <p class="text-muted">
-    This example shows how to put together a basic Machine Learning pipeline. It fetches a dataset from OpenML, trains a variety of machine learning models on a prediction target, and selects the best model based on some evaluation criteria.
+    This example shows how to put together a basic Machine Learning pipeline.
 </p>
 
 ```groovy
@@ -48,11 +48,15 @@ workflow {
 
 </div>
 
+### Synopsis
+
+This example shows how to put together a basic Machine Learning pipeline. It fetches a dataset from OpenML, trains a variety of machine learning models on a prediction target, and selects the best model based on some evaluation criteria.
+
 ### Try it
 
 This pipeline is available on the [nextflow-io/ml-hyperopt](https://github.com/nextflow-io/ml-hyperopt) GitHub repository.
 
-An active internet connection and Docker are required for Nextflow to download the pipeline and necessary images and run the pipeline. The data used by this pipeline will download automatically.
+An active internet connection and Docker are required for Nextflow to download the pipeline and the necessary Docker images to run the pipeline within containers. The data used by this pipeline is stored on the GitHub repository and will download automatically.
 
 To try this pipeline: