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Update after review

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This commit is contained in:
James Fellows Yates 2022-06-02 11:53:53 +02:00
parent a196e0f628
commit d3d28da1b1
4 changed files with 8 additions and 8 deletions
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4
conf/modules.config
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@ -137,8 +137,8 @@ process {
withName: FILTLONG { withName: FILTLONG {
ext.args = [ ext.args = [
"--min_length ${params.longread_qc_minlength}", "--min_length ${params.longread_qc_minlength}",
"--keep_percent ${params.longread_qc_keepbppercent}", "--keep_percent ${params.longread_qc_keep_percent}",
"--target_bases ${params.longread_qc_targetnbases}" "--target_bases ${params.longread_qc_target_bases}"
] ]
.join(' ').trim() .join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" } ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }

4
conf/test.config
View file

@ -24,8 +24,8 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed // 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' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = false perform_longread_qc = true
perform_shortread_complexityfilter = true perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true

4
nextflow.config
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@ -68,8 +68,8 @@ params {
longread_qc_run_clip = false longread_qc_run_clip = false
longread_qc_run_filter = false longread_qc_run_filter = false
longread_qc_minlength = 1000 longread_qc_minlength = 1000
longread_qc_keepbppercent = 90 longread_qc_keep_percent = 90
longread_qc_targetnbases = 500000000 longread_qc_target_bases = 500000000
save_preprocessed_reads = false save_preprocessed_reads = false

4
nextflow_schema.json
View file

@ -420,11 +420,11 @@
"type": "integer", "type": "integer",
"default": 1000 "default": 1000
}, },
"longread_qc_keepbppercent": { "longread_qc_keep_percent": {
"type": "integer", "type": "integer",
"default": 90 "default": 90
}, },
"longread_qc_targetnbases": { "longread_qc_target_bases": {
"type": "integer", "type": "integer",
"default": 500000000 "default": 500000000
} }