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Get recominbing with databases working (still needs cleanup)

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James Fellows Yates 2022-06-21 09:27:07 +02:00
parent bb7323ef1d
commit 7f011477a9
1 changed files with 14 additions and 4 deletions
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18
subworkflows/local/postprocessing_krona.nf
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@ -33,11 +33,22 @@ workflow POSTPROCESSING_KRONA {
// TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS? // TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS?
ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge
.dump(tag: "db_for_kreport_pre") .map{
.join(ch_databases, by: 0) meta, file ->
.dump(tag: "db_for_kreport_post") def db_meta = [ tool: meta.tool, db_name: meta.db_name, db_params: meta.db_params ]
def kfile = file
def sample_meta = [ id: meta.id, run_accession: meta.run_accession, instrument_platform: meta.instrument_platform, single_end: meta.single_end, is_fasta: meta.is_fasta ]
[ db_meta, kfile, sample_meta ]
}
.dump(tag: "sample")
ch_input_for_centrifuge_krona = ch_databases.centrifuge
.collect()
.dump(tag: "db")
.combine(ch_input_for_centrifuge_kreport, by: 0)
.dump(tag: "sm")
// Kraken // Kraken
KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 ) KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 )
KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt ) KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
@ -53,7 +64,6 @@ workflow POSTPROCESSING_KRONA {
KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext) KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext)
ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() ) ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
// Centrifuge // Centrifuge