Main nf whitespace

Dockerfile

@@ -11,7 +11,3 @@ ENV PATH /opt/conda/envs/nf-core-pgdb-1.0.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-pgdb-1.0.0 > nf-core-pgdb-1.0.0.yml
-
-# Instruct R processes to use these empty files instead of clashing with a local version
-RUN touch .Rprofile
-RUN touch .Renviron

conf/test.config

@@ -10,12 +10,12 @@
 params {
   config_profile_name = 'Test profile'
   config_profile_description = 'Minimal test dataset to check pipeline function'
+
   // Limit resources so that this can run on GitHub Actions
   max_cpus = 2
   max_memory = 6.GB
   max_time = 48.h
 
-  single_end = false
   ensembl_name = 'meleagris_gallopavo'
   ensembl = false
   gnomad = false

conf/test_full.config

@@ -12,11 +12,6 @@ params {
   config_profile_description = 'Full test COSMIC generation'
 
   // Input data for full size test
-  single_end = false
-  max_cpus = 2
-  max_memory = 6.GB
-  max_time = 48.h
-
   ensembl_name = 'homo_sapiens'
   ensembl = false
   gnomad = false

docs/usage.md

@@ -17,7 +17,7 @@ nextflow run nf-core/pgdb -profile <docker/singularity/podman/conda/institute> -
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/pgdb --taxonomy 9606 --altorfs -profile docker
+nextflow run nf-core/pgdb --ensembl_name homo_sapiens --altorfs -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.