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Merge pull request #45 from nf-core/run-merging

Re-add run merging
This commit is contained in:
James A. Fellows Yates 2022-04-13 12:27:37 +02:00 committed by GitHub
commit 67d94a9a8d
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8 changed files with 106 additions and 37 deletions

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@ -29,8 +29,8 @@ jobs:
- NXF_VER: ""
NXF_EDGE: "1"
parameters:
- "--longread_clip false"
- "--shortread_clip false"
- "--perform_longread_clip false"
- "--perform_shortread_clipmerge false"
- "--shortread_clipmerge_tool fastp"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
@ -39,6 +39,8 @@ jobs:
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
- "--perform_runmerging"
- "--perform_runmerging --shortread_clipmerge_mergepairs"
steps:
- name: Check out pipeline code

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@ -161,9 +161,19 @@ process {
]
}
withName: CAT_FASTQ {
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/run_merging/" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_runmerged_reads
]
}
withName: MALT_RUN {
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -173,7 +183,7 @@ process {
withName: KRAKEN2_KRAKEN2 {
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: params.publish_dir_mode,
@ -182,12 +192,13 @@ process {
}
withName: METAPHLAN3 {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
mode: params.publish_dir_mode,
pattern: '*.{biom,txt}'
]
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: CENTRIFUGE_CENTRIFUGE {

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@ -28,7 +28,7 @@ params {
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
shortread_clipmerge = true
longread_clip = false
shortread_complexityfilter = true
perform_shortread_clipmerge = true
perform_longread_clip = false
perform_shortread_complexityfilter = true
}

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@ -55,7 +55,7 @@ params {
databases = null
// FASTQ preprocessing
shortread_clipmerge = false
perform_shortread_clipmerge = false
shortread_clipmerge_tool = 'fastp'
shortread_clipmerge_skipadaptertrim = false
shortread_clipmerge_mergepairs = false
@ -63,11 +63,11 @@ params {
shortread_clipmerge_adapter1 = null
shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15
longread_clip = false
perform_longread_clip = false
save_preprocessed_reads = false
// Complexity filtering
shortread_complexityfilter = false
perform_shortread_complexityfilter = false
shortread_complexityfilter_tool = 'bbduk'
shortread_complexityfilter_entropy = 0.3
shortread_complexityfilter_bbduk_windowsize = 50
@ -76,6 +76,9 @@ params {
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false
// run merging
perform_runmerging = false
save_runmerged_reads = false
// MALT
run_malt = false
@ -89,6 +92,7 @@ params {
centrifuge_save_unaligned = false
centrifuge_save_aligned = false
centrifuge_sam_format = false
// metaphlan3
run_metaphlan3 = false
}

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@ -262,15 +262,9 @@
"type": "string",
"default": "None"
},
"shortread_clipmerge": {
"type": "boolean"
},
"shortread_clipmerge_excludeunmerged": {
"type": "boolean"
},
"longread_clip": {
"type": "boolean"
},
"run_malt": {
"type": "boolean"
},
@ -321,8 +315,7 @@
"default": 15
},
"save_preprocessed_reads": {
"type": "boolean",
"default": false
"type": "boolean"
},
"shortread_complexityfilter_tool": {
"type": "string",
@ -335,9 +328,6 @@
"shortread_complexityfilter_bbduk_mask": {
"type": "boolean"
},
"shortread_complexityfilter": {
"type": "boolean"
},
"shortread_complexityfilter_entropy": {
"type": "number",
"default": 0.3
@ -352,8 +342,22 @@
"default": 0.5
},
"save_complexityfiltered_reads": {
"type": "boolean",
"default": false
"type": "boolean"
},
"save_runmerged_reads": {
"type": "boolean"
},
"perform_shortread_clipmerge": {
"type": "boolean"
},
"perform_longread_clip": {
"type": "boolean"
},
"perform_shortread_complexityfilter": {
"type": "boolean"
},
"perform_runmerging": {
"type": "boolean"
}
}
}

View file

@ -9,8 +9,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
workflow PROFILING {
take:
shortreads // [ [ meta ], [ reads ] ]
longreads // [ [ meta ], [ reads ] ]
reads // [ [ meta ], [ reads ] ]
databases // [ [ meta ], path ]
main:
@ -22,8 +21,14 @@ workflow PROFILING {
*/
// 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]
ch_input_for_profiling = shortreads
.mix( longreads )
ch_input_for_profiling = reads
.map {
meta, reads ->
def meta_new = meta.clone()
pairtype = meta_new['single_end'] ? '_se' : '_pe'
meta_new['id'] = meta_new['id'] + pairtype
[meta_new, reads]
}
.combine(databases)
.branch {
malt: it[2]['tool'] == 'malt'

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@ -28,8 +28,8 @@ workflow SHORTREAD_FASTP {
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
meta_new['single_end'] = true
[ meta_new, [ reads ].flatten() ]
}
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )

View file

@ -101,14 +101,14 @@ workflow TAXPROFILER {
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
if ( params.shortread_clipmerge ) {
if ( params.perform_shortread_clipmerge ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
} else {
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
}
if ( params.longread_clip ) {
if ( params.perform_longread_clip ) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] }
} else {
@ -119,17 +119,56 @@ workflow TAXPROFILER {
SUBWORKFLOW: COMPLEXITY FILTERING
*/
if ( params.shortread_complexityfilter ) {
if ( params.perform_shortread_complexityfilter ) {
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
} else {
ch_shortreads_filtered = ch_shortreads_preprocessed
}
/*
STEP: Run merging
*/
if ( params.perform_runmerging ) {
ch_reads_for_cat_branch = ch_shortreads_filtered
.mix( ch_longreads_preprocessed )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new.remove('run_accession')
[ meta_new, reads ]
}
.groupTuple()
.map {
meta, reads ->
[ meta, reads.flatten() ]
}
.branch {
meta, reads ->
// we can't concatenate files if there is not a second run, we branch
// here to separate them out, and mix back in after for efficiency
cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
skip: true
}
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
.mix( ch_reads_for_cat_branch.skip )
.map {
meta, reads ->
[ meta, [ reads ].flatten() ]
}
} else {
ch_reads_runmerged = ch_shortreads_filtered
.mix( ch_longreads_preprocessed )
}
/*
SUBWORKFLOW: PROFILING
*/
PROFILING ( ch_shortreads_filtered, ch_longreads_preprocessed, DB_CHECK.out.dbs )
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
ch_versions = ch_versions.mix( PROFILING.out.versions )
/*
@ -151,21 +190,25 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.shortread_clipmerge) {
if (params.perform_shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
}
if (params.longread_clip) {
if (params.perform_longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
}
if (params.shortread_complexityfilter){
if (params.perform_shortread_complexityfilter){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
}
if (params.perform_runmerging){
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
}
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
// TODO create multiQC module for metaphlan