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https://github.com/MillironX/taxprofiler.git
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Fix cat_fastq naming logic?
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parent
d130a72d74
commit
ca011ccc5b
4 changed files with 45 additions and 17 deletions
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@ -161,9 +161,19 @@ process {
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]
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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]
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.prefix = if params.run_merging : { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -173,7 +183,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = if params.run_merging : { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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@ -182,12 +192,13 @@ process {
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}
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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ext.prefix = if params.run_merging : { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{biom,txt}'
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]
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -78,6 +78,7 @@ params {
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// run merging
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run_merging = false
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save_runmerged_reads = false
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// MALT
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run_malt = false
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@ -10,7 +10,10 @@
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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": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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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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"hidden": true
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},
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"email_on_fail": {
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@ -288,7 +298,10 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -309,8 +322,7 @@
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"default": 15
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},
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"save_preprocessed_reads": {
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"type": "boolean",
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"default": false
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"type": "boolean"
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},
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"shortread_complexityfilter_tool": {
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"type": "string",
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@ -333,15 +345,23 @@
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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": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"default": 0.5
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},
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"save_complexityfiltered_reads": {
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"type": "boolean",
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"default": false
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"type": "boolean"
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},
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"run_merging": {
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"type": "boolean"
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},
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"save_runmerged_reads": {
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"type": "boolean"
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}
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}
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}
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}
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@ -140,10 +140,6 @@ workflow TAXPROFILER {
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[ meta_new, reads ]
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}
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.groupTuple()
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.map {
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meta, reads ->
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[ meta, reads.flatten() ]
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}
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.branch {
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// we can't concate files if there is not a second run, we branch
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// here to separate them out, and mix after
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