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https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
commit
bc84afe80d
3 changed files with 8 additions and 13 deletions
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@ -34,7 +34,7 @@ workflow DB_CHECK {
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emit:
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dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
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versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
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versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
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}
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def create_db_channels(LinkedHashMap row) {
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@ -130,7 +130,7 @@ workflow PROFILING {
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MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
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ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
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}
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@ -111,8 +111,8 @@ workflow TAXPROFILER {
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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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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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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}
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@ -120,7 +120,7 @@ workflow TAXPROFILER {
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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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ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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} else {
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
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}
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@ -131,6 +131,7 @@ workflow TAXPROFILER {
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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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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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} else {
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ch_shortreads_filtered = ch_shortreads_preprocessed
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}
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@ -141,7 +142,7 @@ workflow TAXPROFILER {
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if ( params.perform_shortread_hostremoval ) {
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ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
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} else {
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ch_shortreads_hostremoved = ch_shortreads_filtered
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}
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@ -177,6 +178,8 @@ workflow TAXPROFILER {
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}
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.mix( INPUT_CHECK.out.fasta )
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ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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} else {
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ch_reads_runmerged = ch_shortreads_hostremoved
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.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
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@ -210,26 +213,18 @@ workflow TAXPROFILER {
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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.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.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_shortread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.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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