-
Notifications
You must be signed in to change notification settings - Fork 127
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add test profile for testing provided bowtie index
- Loading branch information
1 parent
0bf058a
commit fff1365
Showing
2 changed files
with
36 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,35 @@ | ||
/* | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Nextflow config file for running minimal tests | ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
Defines input files and everything required to run a fast and simple pipeline test. | ||
Use as follows: | ||
nextflow run nf-core/smrnaseq -profile test_index,<docker/singularity> --outdir <OUTDIR> | ||
---------------------------------------------------------------------------------------- | ||
*/ | ||
|
||
params { | ||
config_profile_name = 'Test index profile' | ||
config_profile_description = 'Minimal test dataset to check pipeline function with bowtie index' | ||
|
||
// Limit resources so that this can run on GitHub Actions | ||
max_cpus = 2 | ||
max_memory = '6.GB' | ||
max_time = '6.h' | ||
|
||
// Input data | ||
|
||
input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv' | ||
fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa' | ||
bowtie_index = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/' | ||
|
||
mirtrace_species = 'hsa' | ||
protocol = 'illumina' | ||
skip_mirdeep = true | ||
save_merged = false | ||
save_aligned_mirna_quant = false | ||
|
||
cleanup = true //Otherwise tests dont run through properly. | ||
} |