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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 {
ext.args = [
"--min_length ${params.longread_qc_minlength}",
"--keep_percent ${params.longread_qc_keepbppercent}",
"--target_bases ${params.longread_qc_targetnbases}"
"--keep_percent ${params.longread_qc_keep_percent}",
"--target_bases ${params.longread_qc_target_bases}"
]
.join(' ').trim()
ext.prefix = { "${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
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true
perform_longread_qc = false
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true

4
nextflow.config
View file

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

4
nextflow_schema.json
View file

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