mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 05:29:54 +00:00
commit
bc84afe80d
3 changed files with 8 additions and 13 deletions
|
@ -34,7 +34,7 @@ workflow DB_CHECK {
|
|||
|
||||
emit:
|
||||
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
|
||||
versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
|
||||
versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
|
||||
}
|
||||
|
||||
def create_db_channels(LinkedHashMap row) {
|
||||
|
|
|
@ -130,7 +130,7 @@ workflow PROFILING {
|
|||
|
||||
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
|
||||
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
|
||||
}
|
||||
|
||||
|
|
|
@ -111,8 +111,8 @@ workflow TAXPROFILER {
|
|||
SUBWORKFLOW: PERFORM PREPROCESSING
|
||||
*/
|
||||
if ( params.perform_shortread_clipmerge ) {
|
||||
|
||||
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
|
||||
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
|
||||
} else {
|
||||
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
|
||||
}
|
||||
|
@ -120,7 +120,7 @@ workflow TAXPROFILER {
|
|||
if ( params.perform_longread_clip ) {
|
||||
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
|
||||
.map { it -> [ it[0], [it[1]] ] }
|
||||
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
|
||||
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
|
||||
} else {
|
||||
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
|
||||
}
|
||||
|
@ -131,6 +131,7 @@ workflow TAXPROFILER {
|
|||
|
||||
if ( params.perform_shortread_complexityfilter ) {
|
||||
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
||||
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
||||
} else {
|
||||
ch_shortreads_filtered = ch_shortreads_preprocessed
|
||||
}
|
||||
|
@ -141,7 +142,7 @@ workflow TAXPROFILER {
|
|||
|
||||
if ( params.perform_shortread_hostremoval ) {
|
||||
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
|
||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
|
||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
||||
} else {
|
||||
ch_shortreads_hostremoved = ch_shortreads_filtered
|
||||
}
|
||||
|
@ -177,6 +178,8 @@ workflow TAXPROFILER {
|
|||
}
|
||||
.mix( INPUT_CHECK.out.fasta )
|
||||
|
||||
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
|
||||
|
||||
} else {
|
||||
ch_reads_runmerged = ch_shortreads_hostremoved
|
||||
.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
|
||||
|
@ -210,26 +213,18 @@ workflow TAXPROFILER {
|
|||
|
||||
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.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.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_shortread_hostremoval) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
|
||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.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 )
|
||||
|
|
Loading…
Reference in a new issue