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https://github.com/MillironX/taxprofiler.git
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Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters
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parent
18886c0cbc
commit
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2 changed files with 42 additions and 11 deletions
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@ -32,7 +32,6 @@ workflow DB_CHECK {
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validate_db_rows(it)
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validate_db_rows(it)
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create_db_channels(it)
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create_db_channels(it)
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}
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}
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.dump(tag: "blah")
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ch_dbs_for_untar = parsed_samplesheet
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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.branch {
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@ -120,17 +120,28 @@ workflow PROFILING {
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}
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}
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if ( params.run_kraken2 ) {
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if ( params.run_kraken2 ) {
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// Have to pick first element of db_params if using bracken,
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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// as db sheet for bracken must have ; sep list to
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.dump(tag: "ch_input_for_kraken2")
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// distinguish between kraken and bracken parameters
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.dump(tag: "ch_input_for_kraken2_b4")
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.map {
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.map {
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// Have to pick first element if using bracken,
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// as db sheet for bracken must have ; sep list to
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meta, reads, db_meta, db ->
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meta, reads, db_meta, db ->
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def db_meta_new = db_meta.clone()
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def db_meta_new = db_meta.clone()
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db_meta_new['db_params'] = db_meta['tool'] == 'bracken' ? db_meta_new['db_params'].split(;)[0] : db_meta_new['db_params']
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// Only take second element if one exists
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def parsed_params = db_meta_new['db_params'].split(";")
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if ( parsed_params.size() == 2 ) {
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db_meta_new['db_params'] = parsed_params[0]
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} else if ( parsed_params.size() == 0 ) {
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db_meta_new['db_params'] = ""
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} else {
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db_meta_new['db_params'] = parsed_params[0]
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}
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[ meta, reads, db_meta_new, db ]
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[ meta, reads, db_meta_new, db ]
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}
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}
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.dump(tag: "ch_input_for_kraken2_after")
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.multiMap {
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.multiMap {
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it ->
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it ->
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reads: [ it[0] + it[2], it[1] ]
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reads: [ it[0] + it[2], it[1] ]
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@ -164,9 +175,6 @@ workflow PROFILING {
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ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report
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ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report
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}
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}
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// TODO UPDATE BRACKEN TO TAKE SECOND ELEMENT OF LIST
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// NEED TO DO CHECKS WHEN ONE OR THE OTHER IS EMPTY AS WELL
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// Extract the database name to combine by.
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// Extract the database name to combine by.
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ch_bracken_databases = databases
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ch_bracken_databases = databases
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.filter { meta, db -> meta['tool'] == 'bracken' }
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.filter { meta, db -> meta['tool'] == 'bracken' }
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@ -176,7 +184,31 @@ workflow PROFILING {
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ch_input_for_bracken = ch_kraken2_output
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ch_input_for_bracken = ch_kraken2_output
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.map { meta, report -> [meta['db_name'], meta, report] }
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.map { meta, report -> [meta['db_name'], meta, report] }
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.combine(ch_bracken_databases, by: 0)
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.combine(ch_bracken_databases, by: 0)
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.dump(tag: "ch_input_for_bracken")
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.dump(tag: "ch_input_for_bracken_b4")
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.map {
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key, meta, reads, db_meta, db ->
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def db_meta_new = db_meta.clone()
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// Have to pick second element if using bracken, as first element
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// contains kraken parameters
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if ( db_meta['tool'] == 'bracken' ) {
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// Only take second element if one exists
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def parsed_params = db_meta_new['db_params'].split(";")
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if ( parsed_params.size() == 2 ) {
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db_meta_new['db_params'] = parsed_params[1]
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} else {
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db_meta_new['db_params'] = ""
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}
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} else {
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db_meta_new['db_params']
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}
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[ key, meta, reads, db_meta_new, db ]
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}
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.dump(tag: "ch_input_for_bracken_after")
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.multiMap { key, meta, report, db_meta, db ->
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.multiMap { key, meta, report, db_meta, db ->
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report: [meta + db_meta, report]
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report: [meta + db_meta, report]
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db: db
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db: db
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