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Ensure alternative long-read processing tools included in tests #526

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merged 4 commits into from
Sep 13, 2024
Merged

Ensure alternative long-read processing tools included in tests #526

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dea8c65
Add nanoq and filtlong to alternative test profile for alternative sh…
jfy133 Sep 12, 2024
76c6372
Fix linting
jfy133 Sep 12, 2024
c04361a
Rename test profile, update all databases to test to 1.2
jfy133 Sep 12, 2024
586514a
Update all the other databases too
jfy133 Sep 12, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -36,7 +36,7 @@ jobs:
- "test_motus"
- "test_falco"
- "test_fastp"
- "test_adapterremoval"
- "test_alternativepreprocessing"
- "test_bbduk"
- "test_prinseqplusplus"

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12 changes: 6 additions & 6 deletions conf/test.config
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Expand Up @@ -11,17 +11,17 @@
*/

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
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 = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
perform_shortread_qc = true
perform_shortread_redundancyestimation = true
perform_longread_qc = true
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54 changes: 0 additions & 54 deletions conf/test_adapterremoval.config
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This file was deleted.

56 changes: 56 additions & 0 deletions conf/test_alternativepreprocessing.config
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@@ -0,0 +1,56 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>

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

params {
config_profile_name = 'Test profile for adapterremoval'
config_profile_description = "Minimal test to check the alternative short-read QC function, adapterremoval"

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_tool = 'adapterremoval'
longread_adapterremoval_tool = 'porechop'
longread_filter_tool = 'filtlong'
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
}

process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
}
}
52 changes: 26 additions & 26 deletions conf/test_bbduk.config
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Expand Up @@ -11,36 +11,36 @@
*/

params {
config_profile_name = 'Test profile for bbduk'
config_profile_description = "Minimal test to check the default tool of short-read complexity filtering, bbduk"
config_profile_name = 'Test profile for bbduk'
config_profile_description = "Minimal test to check the default tool of short-read complexity filtering, bbduk"

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = true
shortread_complexityfilter_tool = 'bbduk'
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = true
shortread_complexityfilter_tool = 'bbduk'
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
}

process {
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52 changes: 26 additions & 26 deletions conf/test_falco.config
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Expand Up @@ -11,36 +11,36 @@
*/

params {
config_profile_name = 'Test profile for Falco'
config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function but running falco instead of fastqc. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
config_profile_name = 'Test profile for Falco'
config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function but running falco instead of fastqc. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
preprocessing_qc_tool = 'falco'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
perform_runmerging = false
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = false
run_kraken2 = false
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
preprocessing_qc_tool = 'falco'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
perform_runmerging = false
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = false
run_kraken2 = false
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
}

process {
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56 changes: 28 additions & 28 deletions conf/test_fastp.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,38 +11,38 @@
*/

params {
config_profile_name = 'Test profile for fastp'
config_profile_description = "Minimal test to check the default short-read QC function, fastp"
config_profile_name = 'Test profile for fastp'
config_profile_description = "Minimal test to check the default short-read QC function, fastp"

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_tool = 'fastp'
perform_shortread_redundancyestimation = true
perform_shortread_complexityfilter = true
shortread_complexityfilter_tool = 'fastp'
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_tool = 'fastp'
perform_shortread_redundancyestimation = true
perform_shortread_complexityfilter = true
shortread_complexityfilter_tool = 'fastp'
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = false
run_malt = false
run_metaphlan = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = false
run_motus = false
run_ganon = false
run_kmcp = false
}

process {
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10 changes: 5 additions & 5 deletions conf/test_full.config
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Expand Up @@ -9,15 +9,15 @@
*/

params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_full.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v1.1.csv'
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_full.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v1.2.csv'

// Genome references
hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'

save_preprocessed_reads = false

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