Improve pipeline overview documentation

[grst]

Description of feature

When looking at the documentation of a new nf-core pipeline, mostly care about two things:

1. What does it do (what kind of input data, which tools, output data)
2. How do I run it (minimal example)

I find it surprisingly hard to quickly find this information for a nf-core pipeline. I sometimes prefer reading the code over reading the documentation.

Here's the documentation website how I perceive it:

(Using RNA-seq as an example, but this applies more generally)

I know there's the usage the parameters sections, which are great, but I'm really missing a quick "getting started" overview for most pipelines.

Alternative suggestion:

(The docs of the rnaseq workflow rewritten, moving boilerplate text into external, linked documents)

Pipeline summary

nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs QC, trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.

[subway map and tools as is]

Usage

If you are new to nextflow and nf-core, please refer to [central documentation page about setting up nextflow] on how to set-up nextflow.

First, you need to prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2,strandedness
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto
CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto
CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto

Each row represents fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically.

Now, you can run the pipeline using:

nextflow run nf-core/rnaseq \
    --input samplesheet.csv \
    --outdir <OUTDIR> \
    --genome GRCh37 \
    -profile <docker/singularity/.../institute>  

For more details, please refer to the usage documentation and the parameter documentation.

Pipeline output

The output of the pipeline applied on an example dataset can be found here [link to AWS test].
For more details, please refer to the output documentation.

Online Videos

[current content as is]

Credits/Support/Citations

[current content as is]

[ewels]

Love it 👍🏻 Maybe even docs with guidelines too? Basically the same as above.

[mirpedrol]

done in #2232