From a8d0e23c0555e6a3e8b5845686118b8a3fd3e625 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?In=C3=AAs=20Mendes?= Date: Tue, 8 Aug 2023 22:23:22 +0100 Subject: [PATCH] [TheiaProk] expose kleborate_virulence_score and kleborate_resistance_score (#146) * expose kleborate_virulence_score and kleborate_resistance_score on theiaprok suit of workflows, and broad_terra_tools * update CI --- tasks/utilities/task_broad_terra_tools.wdl | 4 ++++ tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 6 +++--- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 6 +++--- workflows/theiaprok/wf_theiaprok_fasta.wdl | 4 ++++ workflows/theiaprok/wf_theiaprok_illumina_pe.wdl | 4 ++++ workflows/theiaprok/wf_theiaprok_illumina_se.wdl | 4 ++++ workflows/theiaprok/wf_theiaprok_ont.wdl | 4 ++++ workflows/utilities/wf_merlin_magic.wdl | 2 ++ 8 files changed, 28 insertions(+), 6 deletions(-) diff --git a/tasks/utilities/task_broad_terra_tools.wdl b/tasks/utilities/task_broad_terra_tools.wdl index 393e2b099..708d7bd92 100644 --- a/tasks/utilities/task_broad_terra_tools.wdl +++ b/tasks/utilities/task_broad_terra_tools.wdl @@ -194,6 +194,8 @@ task export_taxon_tables { String? kleborate_otype String? kleborate_klocus_confidence String? kleborate_olocus_confidence + String? kleborate_virulence_score + String? kleborate_resistance_score File? kaptive_output_file_k File? kaptive_output_file_oc String? kaptive_version @@ -508,6 +510,8 @@ task export_taxon_tables { "kleborate_otype": "~{kleborate_otype}", "kleborate_klocus_confidence": "~{kleborate_klocus_confidence}", "kleborate_olocus_confidence": "~{kleborate_olocus_confidence}", + "kleborate_virulence_score": "~{kleborate_virulence_score}", + "kleborate_resistance_score": "~{kleborate_resistance_score}", "ngmaster_tsv": "~{ngmaster_tsv}", "ngmaster_version": "~{ngmaster_version}", "ngmaster_ngmast_sequence_type": "~{ngmaster_ngmast_sequence_type}", diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 0b3445d2e..3ba26335f 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -632,11 +632,11 @@ - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl md5sum: 024971d1439dff7d59c0a26a824bd2c6 - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl - md5sum: f1bcb9e767ae3de776f6218e390bb166 + md5sum: 499eb797a809306edf7e97005f67f8f2 - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl - md5sum: e98bdaa0c00d01b5e77859713ab91689 + md5sum: a76d59109075ce8b861e63ffe70d7c77 - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl - md5sum: ce89635c57ef1bd84a07af59948e80ea + md5sum: 53555c2f3e144e55f362080c5e75e434 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl md5sum: 40d4e09a82030c8219b37f883cddaca4 - path: miniwdl_run/workflow.log diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index 21c5feba9..6d2a6ccbb 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -600,11 +600,11 @@ - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl md5sum: 024971d1439dff7d59c0a26a824bd2c6 - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl - md5sum: f1bcb9e767ae3de776f6218e390bb166 + md5sum: 499eb797a809306edf7e97005f67f8f2 - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl - md5sum: 17be58829cc4e6a1780cf227a2ec99ac + md5sum: c6ab2e13cf4802664b1c93e40a1cd5ba - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl - md5sum: ce89635c57ef1bd84a07af59948e80ea + md5sum: 53555c2f3e144e55f362080c5e75e434 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl md5sum: 53d322d895837c0bcb049786572e944d - path: miniwdl_run/workflow.log diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index dabf5547a..cf4f7df7b 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -270,6 +270,8 @@ workflow theiaprok_fasta { kleborate_otype = merlin_magic.kleborate_otype, kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, ngmaster_tsv = merlin_magic.ngmaster_tsv, ngmaster_version = merlin_magic.ngmaster_version, ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, @@ -512,6 +514,8 @@ workflow theiaprok_fasta { String? kleborate_otype = merlin_magic.kleborate_otype String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence + String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score + String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score # Neisseria gonorrhoeae Typing File? ngmaster_tsv = merlin_magic.ngmaster_tsv String? ngmaster_version = merlin_magic.ngmaster_version diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl index 515f1afa2..e960a7eb1 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl @@ -395,6 +395,8 @@ workflow theiaprok_illumina_pe { kleborate_otype = merlin_magic.kleborate_otype, kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, ngmaster_tsv = merlin_magic.ngmaster_tsv, ngmaster_version = merlin_magic.ngmaster_version, ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, @@ -747,6 +749,8 @@ workflow theiaprok_illumina_pe { String? kleborate_otype = merlin_magic.kleborate_otype String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence + String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score + String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score # Neisseria gonorrhoeae Typing File? ngmaster_tsv = merlin_magic.ngmaster_tsv String? ngmaster_version = merlin_magic.ngmaster_version diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index 742de7637..1d2c80fe5 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -365,6 +365,8 @@ workflow theiaprok_illumina_se { kleborate_otype = merlin_magic.kleborate_otype, kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, ngmaster_tsv = merlin_magic.ngmaster_tsv, ngmaster_version = merlin_magic.ngmaster_version, ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, @@ -696,6 +698,8 @@ workflow theiaprok_illumina_se { String? kleborate_otype = merlin_magic.kleborate_otype String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence + String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score + String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score # Neisseria gonorrhoeae Typing File? ngmaster_tsv = merlin_magic.ngmaster_tsv String? ngmaster_version = merlin_magic.ngmaster_version diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 38f0fc10b..ded5d1807 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -352,6 +352,8 @@ workflow theiaprok_ont { kleborate_otype = merlin_magic.kleborate_otype, kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, ngmaster_tsv = merlin_magic.ngmaster_tsv, ngmaster_version = merlin_magic.ngmaster_version, ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, @@ -653,6 +655,8 @@ workflow theiaprok_ont { String? kleborate_otype = merlin_magic.kleborate_otype String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence + String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score + String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score # Neisseria gonorrhoeae Typing File? ngmaster_tsv = merlin_magic.ngmaster_tsv String? ngmaster_version = merlin_magic.ngmaster_version diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl index 573ca2403..b6fd6e2ae 100644 --- a/workflows/utilities/wf_merlin_magic.wdl +++ b/workflows/utilities/wf_merlin_magic.wdl @@ -518,6 +518,8 @@ workflow merlin_magic { String? kleborate_otype = kleborate.kleborate_otype String? kleborate_klocus_confidence = kleborate.kleborate_klocus_confidence String? kleborate_olocus_confidence = kleborate.kleborate_olocus_confidence + String? kleborate_virulence_score = kleborate.kleborate_virulence_score + String? kleborate_resistance_score = kleborate.kleborate_resistance_score # Neisseria gonorrhoeae Typing File? ngmaster_tsv = ngmaster.ngmaster_tsv String? ngmaster_version = ngmaster.ngmaster_version