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Add KU to the test profiles and add id to KU processes

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This commit is contained in:
James Fellows Yates 2022-11-29 14:19:01 +01:00
parent af8ce2cbfd
commit d7fbe55849
6 changed files with 6 additions and 1 deletions
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1
conf/test.config
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@ -39,6 +39,7 @@ params {
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true
run_krakenuniq = true
run_motus = false run_motus = false
run_krona = true run_krona = true
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab' krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'

1
conf/test_motus.config
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@ -38,6 +38,7 @@ params {
run_metaphlan3 = false run_metaphlan3 = false
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_krakenuniq = false
run_motus = true run_motus = true
run_profile_standardisation = true run_profile_standardisation = true
} }

1
conf/test_nopreprocessing.config
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@ -38,6 +38,7 @@ params {
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true
run_krakenuniq = true
run_motus = false run_motus = false
run_krona = true run_krona = true
} }

1
conf/test_noprofiling.config
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@ -39,6 +39,7 @@ params {
run_metaphlan3 = false run_metaphlan3 = false
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_krakenuniq = false
run_motus = false run_motus = false
} }

1
conf/test_nothing.config
View file

@ -38,6 +38,7 @@ params {
run_metaphlan3 = false run_metaphlan3 = false
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_krakenuniq = false
run_motus = false run_motus = false
} }

2
subworkflows/local/profiling.nf
View file

@ -271,7 +271,7 @@ workflow PROFILING {
ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
.map { .map {
meta, reads, db_meta, db -> meta, reads, db_meta, db ->
[[single_end: meta.single_end], reads, db_meta, db] [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
} }
.groupTuple(by: [0,2,3]) .groupTuple(by: [0,2,3])
.dump(tag: "krakenuniq_premultimap") .dump(tag: "krakenuniq_premultimap")