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Code Issues Releases Packages Activity

Sets correct default for --shortread_qc_mergepairs

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This commit is contained in:
James Fellows Yates 2022-12-06 11:47:16 +01:00
parent 9064584356
commit 3dba6405c5
2 changed files with 2 additions and 3 deletions
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2
nextflow.config
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@ -65,7 +65,7 @@ params {
perform_shortread_qc = false perform_shortread_qc = false
shortread_qc_tool = 'fastp' shortread_qc_tool = 'fastp'
shortread_qc_skipadaptertrim = false shortread_qc_skipadaptertrim = false
shortread_qc_mergepairs = true shortread_qc_mergepairs = false
shortread_qc_includeunmerged = false shortread_qc_includeunmerged = false
shortread_qc_adapter1 = null shortread_qc_adapter1 = null
shortread_qc_adapter2 = null shortread_qc_adapter2 = null

3
nextflow_schema.json
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@ -122,8 +122,7 @@
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turn on merging of read pairs for paired-end data", "description": "Turn on merging of read pairs for paired-end data",
"default": true, "help_text": "Turn on the merging of read-pairs of paired-end short read sequencing data. \n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--collapse`\n> - fastp: `-m --merged_out`\n"
"help_text": "Turn on the merging of read-pairs of paired-end short read sequencing data for AdapterRemoval (this is performed automatically with fastp).\n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--collapse`\n"
}, },
"shortread_qc_includeunmerged": { "shortread_qc_includeunmerged": {
"type": "boolean", "type": "boolean",