Merge pull request #3 from charles-plessy/fusarium

Fusarium test data merged

assets/samplesheet_small.csv

@@ -0,0 +1,3 @@
+sample,fasta
+Fusarium_asiaticum_GCA_025258505.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/258/505/GCA_025258505.1_ASM2525850v1/GCA_025258505.1_ASM2525850v1_genomic.fna.gz
+Fusarium_oxysporum_GCA_014857085.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/857/085/GCA_014857085.1_ASM1485708v1/GCA_014857085.1_ASM1485708v1_genomic.fna.gz

conf/test_small.config

@@ -0,0 +1,34 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/pairgenomealign -profile test_small,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile (small-scale)'
+    config_profile_description = 'Small test dataset using fungal genomes to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '1.h'
+
+    // Input data
+    input = 'assets/samplesheet_small.csv'
+
+    // Target
+    target = 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/258/505/GCA_025258505.1_ASM2525850v1/GCA_025258505.1_ASM2525850v1_genomic.fna.gz'
+    targetName = 'Fusarium_asiaticum_GCA_025258505.1'
+
+    // Do a many-to-many alignment because first query is same as target.
+    m2m = true
+
+    // Genome references
+    genome = 'R64-1-1'
+}

docs/usage.md

@@ -202,6 +202,14 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `test`
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
+- `test_small`
+  - A profile with a complete configuration for small-scale testing
+  - Includes links to two fungal geonomes at NCBI so needs no other parameters
+  - Should take less than 5 min to run and produce meaningful plots
+- `test_full`
+  - A profile with a complete configuration for automated testing at large-scale
+  - Includes links to larger genomes at NCBI so needs no other parameters
+  - Requires larger computational power, useful for stress-testing and real-scale example results
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
 - `singularity`

nextflow.config

@@ -194,6 +194,7 @@ profiles {
         executor.memory         = 8.GB
     }
     test      { includeConfig 'conf/test.config'      }
+    test_small{ includeConfig 'conf/test_small.config'} // Just a pair of fungal genomes
     test_full { includeConfig 'conf/test_full.config' }
 }