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Fix
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parent
1fe9c133f1
commit
139cf0d6aa
2 changed files with 5 additions and 5 deletions
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@ -110,7 +110,7 @@ workflow PROFILING {
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}
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MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log )
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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_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
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ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
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@ -127,7 +127,7 @@ workflow PROFILING {
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}
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KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
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ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
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ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
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@ -185,7 +185,7 @@ workflow PROFILING {
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KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
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KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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@ -227,7 +227,7 @@ workflow PROFILING {
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MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
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ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
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ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
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}
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emit:
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@ -266,7 +266,7 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
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// TODO create multiQC module for metaphlan
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MULTIQC (
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