Fixing typos and clarifying some run options

Author: marchoeppner

docs/installation.md

@@ -1,14 +1,14 @@
 # Installation
 
-## Installation the references
+## Installing the references
 
 This pipeline requires locally stored genomes in fasta format. To build these, do:
 
 ```
 nextflow run marchoeppner/gmo-check -profile standard,singularity --run_name build_refs --outdir /path/to/references
 ```
 
-If you do not singularity on your system, you can also specify docker, podman or conda for software provisioning - see the [usage information](usage.md).
+If you do not have singularity on your system, you can also specify docker, podman or conda for software provisioning - see the [usage information](usage.md).
 
 The path specified with `--outdir` can then be given to the pipeline during normal execution as `--reference_base`.
 

docs/usage.md

@@ -9,7 +9,7 @@ a) Without a site-specific config file
 ```
 nextflow run marchoeppner/gmo-check -profile standard,singularity --input samples.csv --genome tomato --reference_base /path/to/references --run_name pipeline-test
 ```
-where `--path_to_references` corresponds to the location in which you have [installed](installation.md) the pipeline references. 
+where `path_to_references` corresponds to the location in which you have [installed](installation.md) the pipeline references. 
 
 In this example, the pipeline will assume it runs on a single computer with the singularity container engine available. Other options to provision software are:
 
@@ -25,6 +25,8 @@ b) with a site-specific config file
 nextflow run marchoeppner/gmo-check -profile lsh --input samples.csv --genome tomato --run_name pipeline-text
 ```
 
+In this example, both `--reference_base` and the choice of software provisioning are already set in your local configuration and don't have to provided as command line argument. 
+
 # Options
 
 ## `--input samplesheet.csv` [default = null]
@@ -36,7 +38,7 @@ sample_id,library_id,readgroup_id,R1,R2
 S100,S100,AACYTCLM5.1.S100,/home/marc/projects/gaba/data/S100_R1.fastq.gz,/home/marc/projects/gaba/data/S100_R2.fastq.gz
 ```
 
-If you are unsure about the read group ID, just make sure that it should be unique for the combination of library, flowcell and lane. Typically it would be constructed from these components - and the easiest way to get it is from the FastQ file iteself (header of read 1, for example).
+If you are unsure about the readgroup ID, just make sure that it is unique for the combination of library, flowcell and lane. Typically it would be constructed from these components - and the easiest way to get it is from the FastQ file itself (header of read 1, for example).
 
 ## `--genome tomato` [default = tomato]
 
@@ -52,18 +54,22 @@ A mandatory name for this run, to be included with the result files.
 
 ## `--email [email protected]` [ default = null]
 
-An email address to which the MultiQC report is send after pipeline completion. This requires for the executing system to have `sendmail` configured. 
+An email address to which the MultiQC report is send after pipeline completion. This requires for the executing system to have [sendmail](https://rimuhosting.com/support/settingupemail.jsp?mta=sendmail) configured. 
 
 ## `--tools vsearch` [default = vsearch]
 
 This pipeline supports two completely independent tool chains:
 
 - `vsearch` using a simple "metagenomics-like" amplicon processing workflow to produce dereplicated sequences from the short reads to then search for pre-defined patterns against a BLAST database (built-in)
 
-- `bwa2` uses a classical variant calling approach, with parameters similar to what one would find in cancer analysis to detect low-frequency SNPs in mixed samples. 
+- `bwa2` uses a classic variant calling approach, with parameters similar to what one would find in cancer analysis to detect low-frequency SNPs in mixed samples. 
 
 You can specify either one, or both: `--tools 'vsearch,bwa2'` 
 
 ## `--reference_base` [default = null ]
 
-The location of where the pipeline references are installed on your system. This will typically be pre-set in your site-specific config file and is only needed when you run without one. 
+The location of where the pipeline references are installed on your system. This will typically be pre-set in your site-specific config file and is only needed when you run without one. 
+
+## `--outdir results` [default = results]
+
+The location where the results are stored. Usually this will be `results`in the location from where you run the nextflow process. However, this option also accepts any other path in your file system(s).