mirror of
https://github.com/MillironX/taxprofiler.git
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commit
67d94a9a8d
8 changed files with 106 additions and 37 deletions
6
.github/workflows/ci.yml
vendored
6
.github/workflows/ci.yml
vendored
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@ -29,8 +29,8 @@ jobs:
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- NXF_VER: ""
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NXF_EDGE: "1"
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parameters:
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- "--longread_clip false"
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- "--shortread_clip false"
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- "--perform_longread_clip false"
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- "--perform_shortread_clipmerge false"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
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@ -39,6 +39,8 @@ jobs:
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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steps:
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- name: Check out pipeline code
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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 = { "${meta.id}" }
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publishDir = [
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path: { "${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 = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${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 = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${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 = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${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: CENTRIFUGE_CENTRIFUGE {
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@ -28,7 +28,7 @@ params {
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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shortread_clipmerge = true
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longread_clip = false
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shortread_complexityfilter = true
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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}
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@ -55,7 +55,7 @@ params {
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databases = null
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// FASTQ preprocessing
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shortread_clipmerge = false
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perform_shortread_clipmerge = false
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shortread_clipmerge_tool = 'fastp'
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shortread_clipmerge_skipadaptertrim = false
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shortread_clipmerge_mergepairs = false
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@ -63,11 +63,11 @@ params {
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shortread_clipmerge_adapter1 = null
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_minlength = 15
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longread_clip = false
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perform_longread_clip = false
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save_preprocessed_reads = false
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// Complexity filtering
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shortread_complexityfilter = false
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perform_shortread_complexityfilter = false
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shortread_complexityfilter_tool = 'bbduk'
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shortread_complexityfilter_entropy = 0.3
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shortread_complexityfilter_bbduk_windowsize = 50
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@ -76,6 +76,9 @@ params {
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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save_complexityfiltered_reads = false
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// run merging
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perform_runmerging = 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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@ -89,6 +92,7 @@ params {
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centrifuge_save_unaligned = false
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centrifuge_save_aligned = false
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centrifuge_sam_format = false
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// metaphlan3
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run_metaphlan3 = false
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}
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@ -262,15 +262,9 @@
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"type": "string",
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"default": "None"
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},
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"shortread_clipmerge": {
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"type": "boolean"
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},
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"shortread_clipmerge_excludeunmerged": {
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"type": "boolean"
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},
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"longread_clip": {
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"type": "boolean"
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},
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"run_malt": {
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"type": "boolean"
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},
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@ -321,8 +315,7 @@
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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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@ -335,9 +328,6 @@
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"shortread_complexityfilter_bbduk_mask": {
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"type": "boolean"
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},
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"shortread_complexityfilter": {
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"type": "boolean"
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},
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"shortread_complexityfilter_entropy": {
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"type": "number",
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"default": 0.3
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@ -352,8 +342,22 @@
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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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"save_runmerged_reads": {
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"type": "boolean"
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},
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"perform_shortread_clipmerge": {
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"type": "boolean"
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},
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"perform_longread_clip": {
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"type": "boolean"
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},
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"perform_shortread_complexityfilter": {
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"type": "boolean"
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},
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"perform_runmerging": {
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"type": "boolean"
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}
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}
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}
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@ -9,8 +9,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
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workflow PROFILING {
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take:
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shortreads // [ [ meta ], [ reads ] ]
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longreads // [ [ meta ], [ reads ] ]
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reads // [ [ meta ], [ reads ] ]
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databases // [ [ meta ], path ]
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main:
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@ -22,8 +21,14 @@ workflow PROFILING {
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*/
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// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
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ch_input_for_profiling = shortreads
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.mix( longreads )
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ch_input_for_profiling = reads
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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pairtype = meta_new['single_end'] ? '_se' : '_pe'
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meta_new['id'] = meta_new['id'] + pairtype
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[meta_new, reads]
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}
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.combine(databases)
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.branch {
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malt: it[2]['tool'] == 'malt'
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@ -28,8 +28,8 @@ workflow SHORTREAD_FASTP {
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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meta_new['single_end'] = true
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[ meta_new, [ reads ].flatten() ]
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}
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ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
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@ -101,14 +101,14 @@ workflow TAXPROFILER {
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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.shortread_clipmerge ) {
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if ( params.perform_shortread_clipmerge ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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}
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if ( params.longread_clip ) {
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if ( params.perform_longread_clip ) {
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ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
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.map { it -> [ it[0], [it[1]] ] }
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} else {
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@ -119,17 +119,56 @@ workflow TAXPROFILER {
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SUBWORKFLOW: COMPLEXITY FILTERING
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*/
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if ( params.shortread_complexityfilter ) {
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if ( params.perform_shortread_complexityfilter ) {
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ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
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} else {
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ch_shortreads_filtered = ch_shortreads_preprocessed
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}
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/*
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STEP: Run merging
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*/
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if ( params.perform_runmerging ) {
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ch_reads_for_cat_branch = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new.remove('run_accession')
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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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meta, reads ->
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// we can't concatenate files if there is not a second run, we branch
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// here to separate them out, and mix back in after for efficiency
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cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
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skip: true
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}
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ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
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.mix( ch_reads_for_cat_branch.skip )
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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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} else {
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ch_reads_runmerged = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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}
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/*
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SUBWORKFLOW: PROFILING
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*/
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PROFILING ( ch_shortreads_filtered, ch_longreads_preprocessed, DB_CHECK.out.dbs )
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PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( PROFILING.out.versions )
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/*
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@ -151,21 +190,25 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.shortread_clipmerge) {
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if (params.perform_shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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}
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if (params.longread_clip) {
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if (params.perform_longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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}
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if (params.shortread_complexityfilter){
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if (params.perform_shortread_complexityfilter){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.perform_runmerging){
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ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
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// TODO create multiQC module for metaphlan
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