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Formatting and fix fastp output
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ca011ccc5b
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2 changed files with 6 additions and 22 deletions
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@ -10,10 +10,7 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": [
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"input",
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"outdir"
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],
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"required": ["input", "outdir"],
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"properties": {
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"input": {
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"type": "string",
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@ -176,14 +173,7 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"hidden": true
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},
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"email_on_fail": {
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@ -298,10 +288,7 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": [
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"fastp",
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"adapterremoval"
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]
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"enum": ["fastp", "adapterremoval"]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -345,10 +332,7 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": [
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"entropy",
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"dust"
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]
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"enum": ["entropy", "dust"]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -67,7 +67,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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[meta_new, reads]
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}
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.groupTuple()
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.map { meta, fastq -> [meta, fastq.flatten()] }
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.map { meta, fastq -> [meta, [ fastq ].flatten()] }
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CAT_FASTQ(ch_concat_fastq)
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