millironx/taxprofiler
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Merge branch 'dev' into porechop-log

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James A. Fellows Yates 2022-07-26 18:00:28 +00:00
commit 1ef0975736
2 changed files with 5 additions and 5 deletions
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8
subworkflows/local/profiling.nf
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@ -110,7 +110,7 @@ workflow PROFILING {
} }
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary ) MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan ) ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt ) ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
@ -127,7 +127,7 @@ workflow PROFILING {
} }
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification ) KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment ) ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report ) ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
@ -185,7 +185,7 @@ workflow PROFILING {
KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db) KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name) KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() ) ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results ) ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary ) ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
@ -227,7 +227,7 @@ workflow PROFILING {
MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db ) MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() ) ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out ) ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
} }
emit: emit:

2
workflows/taxprofiler.nf
View file

@ -266,7 +266,7 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
} }
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc ) ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
// TODO create multiQC module for metaphlan // TODO create multiQC module for metaphlan
MULTIQC ( MULTIQC (