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Expand tests and fix schema after review

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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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8
.github/workflows/ci.yml vendored
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@ -29,8 +29,16 @@ jobs:
- NXF_VER: "" - NXF_VER: ""
NXF_EDGE: "1" NXF_EDGE: "1"
parameters: parameters:
- "--longread_clip false"
- "--shortread_clip false"
- "--shortread_clipmerge_tool fastp" - "--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_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
steps: steps:
- name: Check out pipeline code - name: Check out pipeline code

1
conf/test.config
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@ -28,5 +28,6 @@ params {
run_malt = true run_malt = true
run_metaphlan3 = true run_metaphlan3 = true
shortread_clipmerge = true shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true shortread_complexityfilter = true
} }

2
nextflow.config
View file

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

3
nextflow_schema.json
View file

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