Fixing installation instructions

Author: marchoeppner

conf/lsh.config

@@ -4,6 +4,8 @@
 params {
 	max_cpus = 40
 	max_ram = 250
+
+  reference_base = "/projects/references/gmo-check"
 }
 
 // Resource manager settings

conf/resources.config

@@ -4,9 +4,9 @@ params {
 
        genomes {
           tomato {
-            fasta    = "${params.reference_base}/solanum_lycopersicum.fa"
-            fai      = "${params.reference_base}/solanum_lycopersicum.fa.fai"
-            dict     = "${params.reference_base}/solanum_lycopersicum.dict"
+            fasta    = "${params.reference_base}/tomato/solanum_lycopersicum.fa"
+            fai      = "${params.reference_base}/tomato/solanum_lycopersicum.fa.fai"
+            dict     = "${params.reference_base}/tomato/solanum_lycopersicum.dict"
             amplicon_txt = "${baseDir}/assets/genomes/tomato/amplicon.txt"
             bed      = "${baseDir}/assets/genomes/tomato/primers.bed"
             target_bed = "${baseDir}/assets/genomes/tomato/targets.bed"

docs/installation.md

@@ -5,7 +5,7 @@
 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
+nextflow run marchoeppner/gmo-check -profile standard,singularity --build_references --run_name build_refs --outdir /path/to/references
 ```
 
 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).

docs/usage.md

@@ -72,4 +72,10 @@ The location of where the pipeline references are installed on your system. This
 
 ## `--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). 
+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). 
+
+## `--freebayes_min_alternate_count 50` [ default = 50]
+The minimum number of reads to support a given SNP. Since we are working with amplicon data, this value can be fairly high. 
+
+## `--freebayes_min_alternate_frac 0.01` [ default = 0.01]
+The minimum percentage of reads supporting a SNP at a given site for the SNP to be considered. The default of 1% is chosen to be able to detect low levels of contribution but may need some tweaking depending on your exact sequencing setup and coverage.