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Code Issues Releases Packages Activity

Remove run merging for now due to complexity

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This commit is contained in:
James Fellows Yates 2022-03-28 16:38:10 +02:00
parent ee53283696
commit 231253227c
3 changed files with 14 additions and 62 deletions
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4
conf/modules.config
View file

@ -105,7 +105,7 @@ process {
pattern: '*.{rma6,tab,text,sam,log}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: KRAKEN2_KRAKEN2 {
@ -115,7 +115,7 @@ process {
pattern: '*.{fastq.gz,txt}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: CUSTOM_DUMPSOFTWAREVERSIONS {

17
subworkflows/local/shortread_fastp.nf
View file

@ -28,15 +28,16 @@ workflow SHORTREAD_FASTP {
FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
if ( params.shortread_clipmerge_mergepairs ) {
// TODO update to replace meta suffix
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
.mix( FASTP_SINGLE.out.reads )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
} else {
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
.mix( FASTP_SINGLE.out.reads )

55
workflows/taxprofiler.nf
View file

@ -116,63 +116,15 @@ workflow TAXPROFILER {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
}
/*
MODULE: PERFORM SHORT READ RUN MERGING
// Remove run accession to allow grouping by sample. Will only merge
// if pairment type is the same.
// TODO Current Branch system currently problematic - when single file not in a list, splits at
// `/` so makes list >= 2, so tries to merge, but then breaks kraken downstream
// e.g. `home jfellows Documents git nf-core taxprofiler testing work 68 9a2c8362add37832a776058d280bb7 2612_se.merged.fastq.gz`
// So theoretically need to force this into a list, (but results the can't access meta.id error as incorrect input format)
// But second issue >= 2 is MAYBE sufficient because what if merging two paired-end files? Need to chcek if the input channel formatted correctly for this? Need to check...
ch_processed_for_combine = ch_shortreads_preprocessed
.dump(tag: "prep_for_combine_grouping")
.map {
meta, reads ->
def meta_new = meta.clone()
// remove run accession to allow group by sample
meta_new.remove('run_accession')
// update id to prevent file name clashes when unable to group
// unmerged PE and SE runs of same sample
def type = meta_new['single_end'] ? "_se" : "_pe"
meta_new['id'] = meta['id'] + type
[ meta_new, reads ]
}
.groupTuple ( by: 0 )
.dump(tag: "files_for_cat_fastq_branch")
.branch{
combine: it[1] && it[1].size() > 1
skip: true
}
// NOTE: this does not allow CATing of SE & PE runs of same sample
// when --shortread_clipmerge_mergepairs is false
ch_processed_for_combine.combine.dump(tag: "input_into_cat_fastq")
CAT_FASTQ ( ch_processed_for_combine.combine )
ch_reads_for_profiling = ch_processed_for_combine.skip
.dump(tag: "skip_combine")
.mix( CAT_FASTQ.out.reads )
.dump(tag: "files_for_profiling")
*/
ch_reads_for_profiling = ch_shortreads_preprocessed
/*
COMBINE READS WITH POSSIBLE DATABASES
*/
// 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 = ch_reads_for_profiling
ch_input_for_profiling = ch_shortreads_preprocessed
.mix( ch_longreads_preprocessed )
.combine(DB_CHECK.out.dbs)
.dump(tag: "reads_plus_db")
.dump(tag: "reads_plus_db_clean")
.branch {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2'
@ -201,12 +153,11 @@ workflow TAXPROFILER {
}
// We can run Kraken2 one-by-one sample-wise
// TODO Only flatten when paired-end! Causing issue commented out above!
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "input_to_kraken")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1].flatten() ]
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}