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Add test configs for krona and concoct #591

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merged 3 commits into from
Feb 16, 2024
Merged

Add test configs for krona and concoct #591

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c6b8546
Turn on Krona in base test
jfy133 Feb 16, 2024
4d0247b
Add CONCOCT test profile and tweak test_nothing metadata
jfy133 Feb 16, 2024
495c719
Add CONCOCT test profile
jfy133 Feb 16, 2024
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1 change: 1 addition & 0 deletions .github/workflows/ci.yml
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Expand Up @@ -62,6 +62,7 @@ jobs:
test_adapterremoval,
test_binrefinement,
test_virus_identification,
test_concoct,
]
steps:
- name: Free some space
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2 changes: 1 addition & 1 deletion conf/test.config
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Expand Up @@ -23,7 +23,7 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv'
centrifuge_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
kraken2_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
skip_krona = true
skip_krona = false
min_length_unbinned_contigs = 1
max_unbinned_contigs = 2
busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
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43 changes: 43 additions & 0 deletions conf/test_concoct.config
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@@ -0,0 +1,43 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Runs input data but skipping all possible steps to allow for a fast testing
profile for input checks etc.

Use as follows:
nextflow run nf-core/mag -profile test_nothing,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Test CONCOCT 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 = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv'
centrifuge_db = null
kraken2_db = null
skip_krona = true
skip_clipping = true
skip_adapter_trimming = false
skip_spades = true
skip_spadeshybrid = true
skip_megahit = false
skip_quast = true
skip_prodigal = true
skip_binning = false
skip_metabat2 = false
skip_maxbin2 = true
skip_concoct = false
skip_prokka = true
skip_binqc = true
skip_gtdbtk = true
gtdbtk_min_completeness = 0
}
2 changes: 1 addition & 1 deletion conf/test_nothing.config
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Expand Up @@ -12,7 +12,7 @@
*/

params {
config_profile_name = 'Test profile'
config_profile_name = 'Test nothing profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
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27 changes: 14 additions & 13 deletions nextflow.config
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Expand Up @@ -302,20 +302,21 @@ profiles {
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_host_rm { includeConfig 'conf/test_host_rm.config' }
test_hybrid { includeConfig 'conf/test_hybrid.config' }
test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
test_busco_auto { includeConfig 'conf/test_busco_auto.config' }
test_ancient_dna { includeConfig 'conf/test_ancient_dna.config' }
test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
test_binning_entry { includeConfig 'conf/test_binning_entry.config' }
test_binrefinement { includeConfig 'conf/test_binrefinement.config' }
test_no_clipping { includeConfig 'conf/test_no_clipping.config' }
test_bbnorm { includeConfig 'conf/test_bbnorm.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_host_rm { includeConfig 'conf/test_host_rm.config' }
test_hybrid { includeConfig 'conf/test_hybrid.config' }
test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
test_busco_auto { includeConfig 'conf/test_busco_auto.config' }
test_ancient_dna { includeConfig 'conf/test_ancient_dna.config' }
test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
test_binning_entry { includeConfig 'conf/test_binning_entry.config' }
test_binrefinement { includeConfig 'conf/test_binrefinement.config' }
test_no_clipping { includeConfig 'conf/test_no_clipping.config' }
test_bbnorm { includeConfig 'conf/test_bbnorm.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_virus_identification { includeConfig 'conf/test_virus_identification.config' }
test_concoct { includeConfig 'conf/test_concoct.config' }
}

// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
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