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Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters

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This commit is contained in:
James Fellows Yates 2023-02-08 13:34:36 +01:00
parent 18886c0cbc
commit fe3d42ffd7
2 changed files with 42 additions and 11 deletions
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1
subworkflows/local/db_check.nf
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@ -32,7 +32,6 @@ workflow DB_CHECK {
validate_db_rows(it)
create_db_channels(it)
}
.dump(tag: "blah")
ch_dbs_for_untar = parsed_samplesheet
.branch {

52
subworkflows/local/profiling.nf
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@ -120,17 +120,28 @@ workflow PROFILING {
}
if ( params.run_kraken2 ) {
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "ch_input_for_kraken2")
// Have to pick first element of db_params if using bracken,
// as db sheet for bracken must have ; sep list to
// distinguish between kraken and bracken parameters
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "ch_input_for_kraken2_b4")
.map {
// Have to pick first element if using bracken,
// as db sheet for bracken must have ; sep list to
meta, reads, db_meta, db ->
def db_meta_new = db_meta.clone()
db_meta_new['db_params'] = db_meta['tool'] == 'bracken' ? db_meta_new['db_params'].split(;)[0] : db_meta_new['db_params']
// Only take second element if one exists
def parsed_params = db_meta_new['db_params'].split(";")
if ( parsed_params.size() == 2 ) {
db_meta_new['db_params'] = parsed_params[0]
} else if ( parsed_params.size() == 0 ) {
db_meta_new['db_params'] = ""
} else {
db_meta_new['db_params'] = parsed_params[0]
}
[ meta, reads, db_meta_new, db ]
}
.dump(tag: "ch_input_for_kraken2_after")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
@ -164,9 +175,6 @@ workflow PROFILING {
ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report
}
// TODO UPDATE BRACKEN TO TAKE SECOND ELEMENT OF LIST
// NEED TO DO CHECKS WHEN ONE OR THE OTHER IS EMPTY AS WELL
// Extract the database name to combine by.
ch_bracken_databases = databases
.filter { meta, db -> meta['tool'] == 'bracken' }
@ -176,7 +184,31 @@ workflow PROFILING {
ch_input_for_bracken = ch_kraken2_output
.map { meta, report -> [meta['db_name'], meta, report] }
.combine(ch_bracken_databases, by: 0)
.dump(tag: "ch_input_for_bracken")
.dump(tag: "ch_input_for_bracken_b4")
.map {
key, meta, reads, db_meta, db ->
def db_meta_new = db_meta.clone()
// Have to pick second element if using bracken, as first element
// contains kraken parameters
if ( db_meta['tool'] == 'bracken' ) {
// Only take second element if one exists
def parsed_params = db_meta_new['db_params'].split(";")
if ( parsed_params.size() == 2 ) {
db_meta_new['db_params'] = parsed_params[1]
} else {
db_meta_new['db_params'] = ""
}
} else {
db_meta_new['db_params']
}
[ key, meta, reads, db_meta_new, db ]
}
.dump(tag: "ch_input_for_bracken_after")
.multiMap { key, meta, report, db_meta, db ->
report: [meta + db_meta, report]
db: db