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Fix MALT save_alignemnts reads and some clean up
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parent
d48b3be5a7
commit
9462032d00
4 changed files with 9 additions and 8 deletions
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@ -47,4 +47,7 @@ process {
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withName: MALT_RUN {
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maxForks = 1
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}
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withName: MEGAN_RMA2INFO {
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maxForks = 1
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}
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}
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@ -196,7 +196,7 @@ profiles {
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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}
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// Load igenomes.config if required
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@ -48,7 +48,7 @@ workflow LONGREAD_PREPROCESSING {
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}
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FASTQC_PROCESSED ( ch_processed_reads.dump(tag: "filtlong") )
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FASTQC_PROCESSED ( ch_processed_reads )
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
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emit:
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@ -66,19 +66,17 @@ workflow PROFILING {
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.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
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.map {
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meta, reads, db_meta, db ->
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def sam_format = params.malt_save_reads ? ' --alignments' : ""
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// TODO No MALT SAM?
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// TODO check all aligned reads published
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// TODO try turning on/off aligned reads
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def sam_format = params.malt_save_reads ? ' --alignments ./ -za false' : ""
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// TODO wut? [9a/a441d6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MALT_RUN (null)
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def temp_meta = [ id: meta['db_name'] ]
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def new_db_meta = db_meta.clone()
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new_db_meta['db_params'] = db_meta['db_params'] + sam_format
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def new_meta = temp_meta + new_db_meta
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new_meta['id'] = new_meta['db_name']
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[ new_meta, reads, db ]
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}
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.groupTuple(by: [0,2])
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.dump(tag: "into_malt")
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.multiMap {
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it ->
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reads: [ it[0], it[1].flatten() ]
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@ -192,7 +190,7 @@ workflow PROFILING {
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// this will replace output file!
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ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format, [] )
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format , [] )
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ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.tsv )
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