Merge pull request #15 from avantonder/dsl2

update for first release

README.md

@@ -1,6 +1,6 @@
 # bacQC
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -34,15 +34,27 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
    tar xvfz minikraken2_v1_8GB_201904.tgz
    ```
-4. An executable Python script called [`fastq_dir_to_samplesheet.py`](https://github.com/avantonder/bacQC/blob/main/bin/fastq_dir_to_samplesheet.py) has been provided and would like to auto-create an input samplesheet based on a directory containing FastQ files **before** you run the pipeline (requires Python 3 installed locally) e.g.
+4. Download the pipeline and test it on a minimal dataset with a single command:
+
+   ```bash
+   nextflow run avantonder/bacQC -profile test,YOURPROFILE --outdir <OUTDIR>
+   ```
+   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+
+   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
+   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+
+5. An executable Python script called [`fastq_dir_to_samplesheet.py`](https://github.com/avantonder/bacQC/blob/main/bin/fastq_dir_to_samplesheet.py) has been provided and would like to auto-create an input samplesheet based on a directory containing FastQ files **before** you run the pipeline (requires Python 3 installed locally) e.g.
 
      ```console
      wget -L https://raw.githubusercontent.com/avantonder/bacQC/main/bin/fastq_dir_to_samplesheet.py
      ./fastq_dir_to_samplesheet.py <FASTQ_DIR> samplesheet.csv -r1 <FWD_FASTQ_SUFFIX> -r2 <REV_FASTQ_SUFFIX> 
      ```
 Alternatively the samplesheet.csv file created by nf-core/fetchngs can also be used.
 
-5. Start running your own analysis!
+6. Start running your own analysis!
 
     - Typical command for QC and species composition
 
@@ -70,13 +82,6 @@ Alternatively the samplesheet.csv file created by nf-core/fetchngs can also be u
         --outdir <OUTDIR>
     ```
 
-    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
-
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
-
 ## Documentation
 
 The avantonder/bacQC pipeline comes with documentation about the pipeline [usage](https://github.com/avantonder/bacQC/blob/main/docs/usage.md), [parameters](https://github.com/avantonder/bacQC/blob/main/docs/parameters.md) and [output](https://github.com/avantonder/bacQC/blob/main/docs/output.md).