millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 14:19:56 +00:00
Code Issues Releases Packages Activity

Merge pull request #107 from nf-core/fix-multiqc-mixing

Browse source 
Fix MultiQC mixing
This commit is contained in:
James A. Fellows Yates 2022-07-26 12:38:52 +02:00 committed by GitHub
commit fdd9a3bc4d
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 5 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

8
subworkflows/local/profiling.nf
View file

@ -110,7 +110,7 @@ workflow PROFILING {
}
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_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
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 )
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_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
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_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_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
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 )
ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
}
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( PROFILING.out.mqc )
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
// TODO create multiQC module for metaphlan
MULTIQC (