Update/docs (#162)

* fix download test

* Update parameters docs

* Update output docs

* drop conda profiles

* update usage docs

Author: matthdsm

.github/workflows/download_pipeline.yml

@@ -95,14 +95,14 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity,s3_ugent --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity,s3_ugent --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards

docs/output.md

@@ -10,7 +10,7 @@ The directories listed below will be created in the results directory after the
 
 ### Sample information
 
-A separate directory will be created in the output directory for each sample containing all output files for that sample.
+A separate directory will be created in the output directory for each sample containing all output files for that sample. If a library name is given in the samplesheet, the sample directories will be nested within a library directory.
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -44,6 +44,7 @@ A separate directory will be created in the output directory for each sample con
   - `SAMPLE.regions.bed.gz`: The regional BED file, showing how well covered the requested regions are, calculated by `mosdepth` (only when a ROI BED file has been given)
   - `SAMPLE.regions.bed.gz.csi`: The index of the regional BED file
   - `SAMPLE.stats`: General statistics for the sample
+  - `multiqc/`: Directory containing the MultiQC report for the sample or library
   </details>
 
 ### Extra outputs for flowcell inputs
@@ -70,20 +71,18 @@ Some additional files will be created when a flowcell input has been used.
 
 </details>
 
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
+[MultiQC](https://seqera.io/multiqc/) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <https://seqera.io/multiqc/>.
 
 ### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `pipeline_info/`
-  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.mmd`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
-  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
-  - Parameters used by the pipeline run: `params.json`.
 
 </details>