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Expand tests and fix schema after review
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4 changed files with 18 additions and 8 deletions
8
.github/workflows/ci.yml
vendored
8
.github/workflows/ci.yml
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@ -29,8 +29,16 @@ jobs:
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- NXF_VER: ""
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- NXF_VER: ""
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NXF_EDGE: "1"
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NXF_EDGE: "1"
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parameters:
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parameters:
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- "--longread_clip false"
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- "--shortread_clip false"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
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- "--shortread_clipmerge_tool adapterremoval"
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- "--shortread_clipmerge_tool adapterremoval"
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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steps:
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steps:
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- name: Check out pipeline code
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- name: Check out pipeline code
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@ -22,11 +22,12 @@ params {
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// Input data
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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run_kraken2 = true
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run_kraken2 = true
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run_malt = true
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run_malt = true
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run_metaphlan3 = true
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run_metaphlan3 = true
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shortread_clipmerge = true
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shortread_clipmerge = true
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longread_clip = false
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shortread_complexityfilter = true
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shortread_complexityfilter = true
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}
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}
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@ -51,7 +51,7 @@ params {
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max_cpus = 16
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max_cpus = 16
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max_time = '240.h'
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max_time = '240.h'
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// Databaess
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// Databases
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databases = null
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databases = null
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// FASTQ preprocessing
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// FASTQ preprocessing
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@ -328,7 +328,8 @@
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},
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},
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"type": "string",
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"default": "entropy"
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"default": "entropy",
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"enum": ["entropy", "dust"]
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},
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"type": "number",
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