Merge pull request #491 from nf-core/docs-updates

Docs and tutorials updates

Author: apeltzer

.github/markdownlint.yml

@@ -8,3 +8,5 @@ no-inline-html:
         - img
         - p
         - kbd
+        - details
+        - summary

README.md

@@ -45,6 +45,10 @@ By default the pipeline currently performs the following:
 
 Additional functionality contained by the pipeline currently includes:
 
+#### Input
+
+* Automatic merging of complex sequencing setups (e.g. multiple lanes, sequencing configurations, library types)
+
 #### Preprocessing
 
 * Illumina two-coloured sequencer poly-G tail removal (`fastp`)

assets/multiqc_config.yaml

@@ -93,7 +93,6 @@ top_modules:
     - 'mtnucratio'
     - 'qualimap'
     - 'sexdeterrmine'
-    - 'gatk'
     - 'multivcfanalyzer':
        path_filters:
            - '*MultiVCFAnalyzer.json'

docs/README.md

@@ -14,3 +14,5 @@ The nf-core/eager documentation is split into the following files:
    1. This covers common nf-core errors
 7. [Frequently Asked Questions](faq.md)
    1. This covers more specific nf-core/eager errors
+8. Tutorials
+   1. [How to write and use profiles for sharing your settings and reproducible science!](tutorial_profiles.md)

docs/code_contribution.md

@@ -141,3 +141,11 @@ You then need to edit the script `bin/scrape_software_versions.py` to
 2. add a HTML block entry to the `OrderedDict` for formatting in MultiQC.
 
 > If a tool does not unfortunately offer any printing of version data, you may add this 'manually' e.g. with `echo "v1.1" > v_<YOUR_TOOL>.txt`
+
+## Images and Figures
+
+For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License.
+
+For the overview image we follow the nf-core [style and guidelines](https://nf-co.re/developers/design_guidelines).
+
+These can be found for download [here](https://fonts.google.com/specimen/Kalam)

docs/faq.md

@@ -20,6 +20,30 @@ Specifying the version of the run you are using is highly recommended, as it hel
 
 You can see more information on the nextflow documentation [here](https://www.nextflow.io/docs/latest/sharing.html?highlight=revision#handling-revisions).
 
+## I am only getting output for a single sample although I specified multiple with wildcards
+
+You must specify paths to files in quotes, otherwise your shell will evaluate any wildcards (\*) rather than Nextflow.
+
+For example
+
+```bash
+nextflow run nf-core/eager --input /path/to/sample_*/*.fq.gz
+```
+
+Would be evaluated by your shell as  
+
+```bash
+nextflow run nf-core/eager --input /path/to/sample_1/sample_1.fq.gz /path/to/sample_1/sample_1.fq.gz /path/to/sample_1/sample_1.fq.gz
+```
+
+And Nextflow will only take the first path after `--input`, ignoring the others.
+
+On the otherhand encapsulating the path in quotes will allow Nextflow to evaluate the paths.
+
+```bash
+nextflow run nf-core/eager --input "/path/to/sample_*/*.fq.gz"
+```
+
 ## I specified a module and it didn't produce the expected output
 
 Possible options: