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Main nf whitespace #28

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Apr 15, 2021
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4 changes: 0 additions & 4 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion conf/test.config
Original file line number Diff line number Diff line change
Expand Up @@ -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
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5 changes: 0 additions & 5 deletions conf/test_full.config
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.
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