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Expand tests and fix schema after review

This commit is contained in:
James Fellows Yates 2022-04-05 11:04:30 +02:00
parent bb6dd738bd
commit d46ddd972c
4 changed files with 18 additions and 8 deletions

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@ -29,8 +29,16 @@ jobs:
- NXF_VER: ""
NXF_EDGE: "1"
parameters:
- "--longread_clip false"
- "--shortread_clip false"
- "--shortread_clipmerge_tool fastp"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
- "--shortread_clipmerge_tool adapterremoval"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
steps:
- name: Check out pipeline code

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@ -22,11 +22,12 @@ params {
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true
run_metaphlan3 = true
shortread_clipmerge = true
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true
run_metaphlan3 = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true
}

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@ -51,7 +51,7 @@ params {
max_cpus = 16
max_time = '240.h'
// Databaess
// Databases
databases = null
// FASTQ preprocessing

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@ -328,7 +328,8 @@
},
"shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string",
"default": "entropy"
"default": "entropy",
"enum": ["entropy", "dust"]
},
"shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number",