diff --git a/CHANGELOG.md b/CHANGELOG.md index 63861478..bb90493b 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ Code contributions to the release: - Remove wrapper from github actions (test_sftp_modules) [#421](https://github.com/BU-ISCIII/relecov-tools/pull/421) - Add Validation for Dropdown Columns: Notify Users of Invalid Entries in build-schema module [#423](https://github.com/BU-ISCIII/relecov-tools/pull/423) - Test SFTP Login by Updating Port Assignment in wrapper_manager [#426](https://github.com/BU-ISCIII/relecov-tools/pull/426) +- Update Test Data for new Schema & Modify JSON Filepaths in read-bioinfo-metadata [#427](https://github.com/BU-ISCIII/relecov-tools/pull/427) #### Fixes diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 2abc28fe..5ad8114d 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -106,6 +106,7 @@ "multiple_samples": true, "required": true, "function": null, + "extract": true, "content": { "ns_per_100_kbp": "# Ns per 100kb consensus" } @@ -122,6 +123,7 @@ "required": true, "multiple_samples": true, "function": null, + "extract": true, "content": { "software_version": { "bioinformatics_protocol_software_version": "nf-core/viralrecon", diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 7b8cd08e..9cb4f796 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -20,7 +20,7 @@ }, "metadata_lab_heading": [ "Organism", - "Public Health sample id (SIVIES)", + "Public Health sample id (SIVIRA)", "Sample ID given by originating laboratory", "Sample ID given by the submitting laboratory", "Sample ID given in the microbiology lab", @@ -41,7 +41,8 @@ "Environmental System", "Collection Device", "Host", - "Host Age", + "Host Age Years", + "Host Age Months", "Host Gender", "Sequencing Date", "Nucleic acid extraction protocol", @@ -66,7 +67,13 @@ "Diagnostic Pcr Ct Value-2", "Authors", "Sequence file R1 fastq", - "Sequence file R2 fastq" + "Sequence file R2 fastq", + "Vaccinated", + "Specific medication for treatment or prophylaxis", + "Hospitalization", + "Admission to intensive care unit", + "Death", + "Immunosuppression" ], "alt_heading_equivalences": { "Sample ID": "Sample ID given for sequencing", diff --git a/relecov_tools/dataprocess_wrapper.py b/relecov_tools/dataprocess_wrapper.py index 8a0f3305..92a01f9f 100644 --- a/relecov_tools/dataprocess_wrapper.py +++ b/relecov_tools/dataprocess_wrapper.py @@ -73,7 +73,12 @@ def clean_module_params(self, module, params): return module_valid_params def exec_download(self, download_params): + if "sftp_port" in download_params: + sftp_port = download_params.pop("sftp_port", None) download_manager = DownloadManager(**download_params) + if sftp_port is not None: + download_manager.relecov_sftp.sftp_port = int(sftp_port) + print(f"SFTP port assigned: {download_manager.relecov_sftp.sftp_port}") download_manager.execute_process() finished_folders = download_manager.finished_folders download_logs = self.wrapper_logsum.prepare_final_logs( diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 809adc18..4688ac58 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -344,8 +344,11 @@ def read_metadata_file(self, meta_f_path, return_data=True): error_text = "Header could not be found for excel file %s" raise MetadataError(str(error_text % os.path.basename(meta_f_path))) for cell in ws_metadata_lab[header_row]: - cell.value = cell.value.strip() - metadata_header = [x.value for x in ws_metadata_lab[header_row]] + if cell.value is not None: + cell.value = cell.value.strip() + metadata_header = [ + x.value for x in ws_metadata_lab[header_row] if x.value is not None + ] meta_column_list = self.metadata_lab_heading if meta_column_list != metadata_header[1:]: diffs = [ diff --git a/relecov_tools/example_data/1.read_lab_metadata_module/sample_data.json b/relecov_tools/example_data/1.read_lab_metadata_module/sample_data.json index 79981d15..05d86076 100644 --- a/relecov_tools/example_data/1.read_lab_metadata_module/sample_data.json +++ b/relecov_tools/example_data/1.read_lab_metadata_module/sample_data.json @@ -2,24 +2,24 @@ "210141": { "fastq_r1_md5": "eab8b05ef27f4f5cba5cddf6ad627de2", "fastq_r2_md5": "d82a37aa970df2b8bf8f547ca7c18ac8", - "r1_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "sequence_file_R1_fastq": "210141_R1.fastq.gz", "sequence_file_R2_fastq": "210141_R2.fastq.gz" }, "2018086": { "fastq_r1_md5": "b5242d60471e5a5a97b35531dbbe8c30", "fastq_r2_md5": "57525c5a1ec992098e652aa01b366d69", - "r1_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "sequence_file_R1_fastq": "2018086_R1.fastq.gz", "sequence_file_R2_fastq": "2018086_R2.fastq.gz" }, "2018102": { "fastq_r1_md5": "b5242d60471e5a5a97b35531dbbe8c30", "fastq_r2_md5": "57525c5a1ec992098e652aa01b366d69", - "r1_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/media/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/media/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "sequence_file_R1_fastq": "2018102_R1.fastq.gz", "sequence_file_R2_fastq": "2018102_R2.fastq.gz" } diff --git a/relecov_tools/example_data/2.validate_module/processed_metadata_lab.json b/relecov_tools/example_data/2.validate_module/processed_metadata_lab.json index 5b11ba10..30893092 100644 --- a/relecov_tools/example_data/2.validate_module/processed_metadata_lab.json +++ b/relecov_tools/example_data/2.validate_module/processed_metadata_lab.json @@ -52,8 +52,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018086_R1.fastq.gz_2018086_R2.fastq.gz", @@ -132,8 +132,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018102_R1.fastq.gz_2018102_R2.fastq.gz", @@ -212,8 +212,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018109_R1.fastq.gz_2018109_R2.fastq.gz", diff --git a/relecov_tools/example_data/3.map_module/processed_metadata_lab.json b/relecov_tools/example_data/3.map_module/processed_metadata_lab.json index 5b11ba10..30893092 100644 --- a/relecov_tools/example_data/3.map_module/processed_metadata_lab.json +++ b/relecov_tools/example_data/3.map_module/processed_metadata_lab.json @@ -52,8 +52,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018086_R1.fastq.gz_2018086_R2.fastq.gz", @@ -132,8 +132,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018102_R1.fastq.gz_2018102_R2.fastq.gz", @@ -212,8 +212,8 @@ "number_of_samples_in_run": "", "organism": "Severe acute respiratory syndrome coronavirus 2", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "2018109_R1.fastq.gz_2018109_R2.fastq.gz", diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json index 01c8ef58..77119f3f 100644 --- a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json +++ b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json @@ -12,7 +12,7 @@ "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -31,7 +31,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -68,7 +68,7 @@ "consensus_sequence_R1_name": "214822_S13_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f0bf2700ae3eadc9a3f01c515546bf4a", "consensus_sequence_R2_name": "214822_S13_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -87,7 +87,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -124,7 +124,7 @@ "consensus_sequence_R1_name": "214823_S1_R1_001.fastq.gz", "consensus_sequence_R2_md5": "1b58f58f861c81ed94401a319c7ae9ce", "consensus_sequence_R2_name": "214823_S1_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -143,7 +143,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "nan", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -180,7 +180,7 @@ "consensus_sequence_R1_name": "214824_S14_R1_001.fastq.gz", "consensus_sequence_R2_md5": "eebdabee75e327f49d9e1741d22c40c3", "consensus_sequence_R2_name": "214824_S14_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -199,7 +199,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "nan", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -236,7 +236,7 @@ "consensus_sequence_R1_name": "214825_S15_R1_001.fastq.gz", "consensus_sequence_R2_md5": "7356129837732007e08e94a7699c5f7e", "consensus_sequence_R2_name": "214825_S15_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -255,7 +255,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -292,7 +292,7 @@ "consensus_sequence_R1_name": "214826_S16_R1_001.fastq.gz", "consensus_sequence_R2_md5": "3c245df1ecc9456ab121337847a8282d", "consensus_sequence_R2_name": "214826_S16_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -311,7 +311,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -348,7 +348,7 @@ "consensus_sequence_R1_name": "214827_S17_R1_001.fastq.gz", "consensus_sequence_R2_md5": "b95ddabc2cb0337a225c7998ec3a11fd", "consensus_sequence_R2_name": "214827_S17_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -367,7 +367,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -404,7 +404,7 @@ "consensus_sequence_R1_name": "214828_S18_R1_001.fastq.gz", "consensus_sequence_R2_md5": "fa80eea72d21d5d686af19b779e00cd7", "consensus_sequence_R2_name": "214828_S18_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -423,7 +423,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -460,7 +460,7 @@ "consensus_sequence_R1_name": "214829_S19_R1_001.fastq.gz", "consensus_sequence_R2_md5": "047dd05f8008dc7fa0c9f2c5d7f51677", "consensus_sequence_R2_name": "214829_S19_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -479,7 +479,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -516,7 +516,7 @@ "consensus_sequence_R1_name": "214830_S20_R1_001.fastq.gz", "consensus_sequence_R2_md5": "345fadf48d0f1b4e14951d82145f985a", "consensus_sequence_R2_name": "214830_S20_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -535,7 +535,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -572,7 +572,7 @@ "consensus_sequence_R1_name": "214831_S21_R1_001.fastq.gz", "consensus_sequence_R2_md5": "5414313cf3edb5bc6ab9c74a81237277", "consensus_sequence_R2_name": "214831_S21_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -591,7 +591,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -628,7 +628,7 @@ "consensus_sequence_R1_name": "214832_S22_R1_001.fastq.gz", "consensus_sequence_R2_md5": "7e8ee7de84d4a0c83da2fa4d86744795", "consensus_sequence_R2_name": "214832_S22_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -647,7 +647,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "nan", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -684,7 +684,7 @@ "consensus_sequence_R1_name": "214833_S23_R1_001.fastq.gz", "consensus_sequence_R2_md5": "634d553b612db4a272537b445827c3ae", "consensus_sequence_R2_name": "214833_S23_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -703,7 +703,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -740,7 +740,7 @@ "consensus_sequence_R1_name": "214834_S24_R1_001.fastq.gz", "consensus_sequence_R2_md5": "71b565731008044ca6115528230b1bcc", "consensus_sequence_R2_name": "214834_S24_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -759,7 +759,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -796,7 +796,7 @@ "consensus_sequence_R1_name": "214835_S25_R1_001.fastq.gz", "consensus_sequence_R2_md5": "8208d8f05c4dd2dedc7f8b017d1f00b4", "consensus_sequence_R2_name": "214835_S25_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -815,7 +815,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -852,7 +852,7 @@ "consensus_sequence_R1_name": "214836_S26_R1_001.fastq.gz", "consensus_sequence_R2_md5": "5addc2c98ff7d6458a4b319e25731654", "consensus_sequence_R2_name": "214836_S26_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -871,7 +871,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -908,7 +908,7 @@ "consensus_sequence_R1_name": "214837_S27_R1_001.fastq.gz", "consensus_sequence_R2_md5": "17670b749961800dfdc995cf3c4c6faf", "consensus_sequence_R2_name": "214837_S27_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -927,7 +927,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -964,7 +964,7 @@ "consensus_sequence_R1_name": "214838_S2_R1_001.fastq.gz", "consensus_sequence_R2_md5": "6cddef3197226f00bd7eb8c437e94900", "consensus_sequence_R2_name": "214838_S2_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -983,7 +983,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1020,7 +1020,7 @@ "consensus_sequence_R1_name": "220338_S3_R1_001.fastq.gz", "consensus_sequence_R2_md5": "6ab5c2b6fa4005479da188e7bb7d584b", "consensus_sequence_R2_name": "220338_S3_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1039,7 +1039,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1076,7 +1076,7 @@ "consensus_sequence_R1_name": "220339_S4_R1_001.fastq.gz", "consensus_sequence_R2_md5": "391b790d0d105fd9e8c6c037df8a18d4", "consensus_sequence_R2_name": "220339_S4_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1095,7 +1095,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1132,7 +1132,7 @@ "consensus_sequence_R1_name": "220407_S5_R1_001.fastq.gz", "consensus_sequence_R2_md5": "1400d0c52ad2dc2231c1fe87e0bd1dde", "consensus_sequence_R2_name": "220407_S5_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1151,7 +1151,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1188,7 +1188,7 @@ "consensus_sequence_R1_name": "220433_S6_R1_001.fastq.gz", "consensus_sequence_R2_md5": "3d39eeffbd2983251f7153b1792cb865", "consensus_sequence_R2_name": "220433_S6_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1207,7 +1207,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1244,7 +1244,7 @@ "consensus_sequence_R1_name": "220518_S7_R1_001.fastq.gz", "consensus_sequence_R2_md5": "9884025a080d74f187017475c2e140f7", "consensus_sequence_R2_name": "220518_S7_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1263,7 +1263,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1300,7 +1300,7 @@ "consensus_sequence_R1_name": "220529_S28_R1_001.fastq.gz", "consensus_sequence_R2_md5": "38ce949c2a98a1bf4dbcd444483860e1", "consensus_sequence_R2_name": "220529_S28_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1319,7 +1319,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1356,7 +1356,7 @@ "consensus_sequence_R1_name": "220530_S29_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f474a72ba984af48d96b95ee3d9201a6", "consensus_sequence_R2_name": "220530_S29_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1375,7 +1375,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1412,7 +1412,7 @@ "consensus_sequence_R1_name": "220531_S30_R1_001.fastq.gz", "consensus_sequence_R2_md5": "e0b1d1d6557f03cfca04005721244270", "consensus_sequence_R2_name": "220531_S30_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1431,7 +1431,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.18", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1468,7 +1468,7 @@ "consensus_sequence_R1_name": "220532_S31_R1_001.fastq.gz", "consensus_sequence_R2_md5": "fc770dc2431972bf859d64b3fb7b24cd", "consensus_sequence_R2_name": "220532_S31_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1487,7 +1487,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1524,7 +1524,7 @@ "consensus_sequence_R1_name": "220533_S32_R1_001.fastq.gz", "consensus_sequence_R2_md5": "e752ffb157d139701ecf2e765ce4642f", "consensus_sequence_R2_name": "220533_S32_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1543,7 +1543,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1580,7 +1580,7 @@ "consensus_sequence_R1_name": "220534_S33_R1_001.fastq.gz", "consensus_sequence_R2_md5": "632355ba64f7de8c471d98028394a792", "consensus_sequence_R2_name": "220534_S33_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1599,7 +1599,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1636,7 +1636,7 @@ "consensus_sequence_R1_name": "220535_S34_R1_001.fastq.gz", "consensus_sequence_R2_md5": "38ad2aaf11d71d43e8c9e2996419c9c7", "consensus_sequence_R2_name": "220535_S34_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1655,7 +1655,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1692,7 +1692,7 @@ "consensus_sequence_R1_name": "220536_S35_R1_001.fastq.gz", "consensus_sequence_R2_md5": "95540b3c187f2be5b390e028a53744f0", "consensus_sequence_R2_name": "220536_S35_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1711,7 +1711,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1748,7 +1748,7 @@ "consensus_sequence_R1_name": "220537_S36_R1_001.fastq.gz", "consensus_sequence_R2_md5": "ba90ceea113af1b1154cfc88791130f4", "consensus_sequence_R2_name": "220537_S36_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1767,7 +1767,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1804,7 +1804,7 @@ "consensus_sequence_R1_name": "220538_S37_R1_001.fastq.gz", "consensus_sequence_R2_md5": "001cde855df87b0bd1a53ee2f2b6b3ef", "consensus_sequence_R2_name": "220538_S37_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1823,7 +1823,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.18", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1860,7 +1860,7 @@ "consensus_sequence_R1_name": "220539_S38_R1_001.fastq.gz", "consensus_sequence_R2_md5": "3b9d109620122fe4f8d0395474cffa73", "consensus_sequence_R2_name": "220539_S38_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1879,7 +1879,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1916,7 +1916,7 @@ "consensus_sequence_R1_name": "220540_S39_R1_001.fastq.gz", "consensus_sequence_R2_md5": "ad64eff1e7994f31758f3539a68ee8f4", "consensus_sequence_R2_name": "220540_S39_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1935,7 +1935,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -1972,7 +1972,7 @@ "consensus_sequence_R1_name": "220541_S40_R1_001.fastq.gz", "consensus_sequence_R2_md5": "79ec4ae16bfedc05b0ed0d2ab1cf5dc3", "consensus_sequence_R2_name": "220541_S40_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -1991,7 +1991,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2028,7 +2028,7 @@ "consensus_sequence_R1_name": "220542_S41_R1_001.fastq.gz", "consensus_sequence_R2_md5": "11e101b892f6429d4762f7e8acb8f8fa", "consensus_sequence_R2_name": "220542_S41_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2047,7 +2047,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2084,7 +2084,7 @@ "consensus_sequence_R1_name": "220543_S42_R1_001.fastq.gz", "consensus_sequence_R2_md5": "761f5cf6ec9e70a3c6052e6717181987", "consensus_sequence_R2_name": "220543_S42_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2103,7 +2103,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2140,7 +2140,7 @@ "consensus_sequence_R1_name": "220544_S43_R1_001.fastq.gz", "consensus_sequence_R2_md5": "354eb8ebd7da78d0e4061ff45510b247", "consensus_sequence_R2_name": "220544_S43_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2159,7 +2159,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2196,7 +2196,7 @@ "consensus_sequence_R1_name": "220545_S44_R1_001.fastq.gz", "consensus_sequence_R2_md5": "45f3f30a76c6c9099cc10a54a55326ac", "consensus_sequence_R2_name": "220545_S44_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2215,7 +2215,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2252,7 +2252,7 @@ "consensus_sequence_R1_name": "220546_S45_R1_001.fastq.gz", "consensus_sequence_R2_md5": "e03a1e702b7b0ff54bb57f95e47e99a2", "consensus_sequence_R2_name": "220546_S45_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2271,7 +2271,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2308,7 +2308,7 @@ "consensus_sequence_R1_name": "220599_S8_R1_001.fastq.gz", "consensus_sequence_R2_md5": "b0bf94bbd7290a0b2193025cda14dc02", "consensus_sequence_R2_name": "220599_S8_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2327,7 +2327,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2364,7 +2364,7 @@ "consensus_sequence_R1_name": "220600_S9_R1_001.fastq.gz", "consensus_sequence_R2_md5": "ba22af6782ec196a43e76cec80a36741", "consensus_sequence_R2_name": "220600_S9_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2383,7 +2383,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "nan", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2420,7 +2420,7 @@ "consensus_sequence_R1_name": "220601_S10_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f395c916a68376183577b7810af918bc", "consensus_sequence_R2_name": "220601_S10_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2439,7 +2439,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2476,7 +2476,7 @@ "consensus_sequence_R1_name": "220603_S11_R1_001.fastq.gz", "consensus_sequence_R2_md5": "aed63e4ee67de18ce6ff50c0a2fa3674", "consensus_sequence_R2_name": "220603_S11_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2495,7 +2495,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "nan", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2532,7 +2532,7 @@ "consensus_sequence_R1_name": "220624_S46_R1_001.fastq.gz", "consensus_sequence_R2_md5": "d0cd564bec34963ef961abfc7e9206fa", "consensus_sequence_R2_name": "220624_S46_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2551,7 +2551,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2588,7 +2588,7 @@ "consensus_sequence_R1_name": "220625_S47_R1_001.fastq.gz", "consensus_sequence_R2_md5": "a2f2cd43085caa4b198b5b7ffa0b0a09", "consensus_sequence_R2_name": "220625_S47_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2607,7 +2607,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2644,7 +2644,7 @@ "consensus_sequence_R1_name": "220626_S48_R1_001.fastq.gz", "consensus_sequence_R2_md5": "1c57c19841c6d25daa917135696dfabb", "consensus_sequence_R2_name": "220626_S48_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2663,7 +2663,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2700,7 +2700,7 @@ "consensus_sequence_R1_name": "220627_S49_R1_001.fastq.gz", "consensus_sequence_R2_md5": "e4fbdcea92c7e7e762c494bdec1216dc", "consensus_sequence_R2_name": "220627_S49_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2719,7 +2719,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2756,7 +2756,7 @@ "consensus_sequence_R1_name": "220628_S50_R1_001.fastq.gz", "consensus_sequence_R2_md5": "5ecbf9332f8f085bca8ff71095161d27", "consensus_sequence_R2_name": "220628_S50_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2775,7 +2775,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.15.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2812,7 +2812,7 @@ "consensus_sequence_R1_name": "220629_S51_R1_001.fastq.gz", "consensus_sequence_R2_md5": "c243d5d71e4dab63d4b5e5399c9336ae", "consensus_sequence_R2_name": "220629_S51_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2831,7 +2831,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2868,7 +2868,7 @@ "consensus_sequence_R1_name": "220630_S52_R1_001.fastq.gz", "consensus_sequence_R2_md5": "df070c9a8e583211f198bc67bb16b3bc", "consensus_sequence_R2_name": "220630_S52_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2887,7 +2887,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2924,7 +2924,7 @@ "consensus_sequence_R1_name": "220631_S53_R1_001.fastq.gz", "consensus_sequence_R2_md5": "ca6a1e4503d3892e60f86b24ac26e7c1", "consensus_sequence_R2_name": "220631_S53_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2943,7 +2943,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "AY.127", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -2980,7 +2980,7 @@ "consensus_sequence_R1_name": "220633_S54_R1_001.fastq.gz", "consensus_sequence_R2_md5": "33c3e32357450b511a5657b0c22aa9fb", "consensus_sequence_R2_name": "220633_S54_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -2999,7 +2999,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3036,7 +3036,7 @@ "consensus_sequence_R1_name": "220634_S55_R1_001.fastq.gz", "consensus_sequence_R2_md5": "a49c009e9eeb68c46b8dafd0da05eadb", "consensus_sequence_R2_name": "220634_S55_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3055,7 +3055,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3092,7 +3092,7 @@ "consensus_sequence_R1_name": "220635_S56_R1_001.fastq.gz", "consensus_sequence_R2_md5": "51bf5c329fc240c8e8f1baefc37d5c1b", "consensus_sequence_R2_name": "220635_S56_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3111,7 +3111,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3148,7 +3148,7 @@ "consensus_sequence_R1_name": "220636_S57_R1_001.fastq.gz", "consensus_sequence_R2_md5": "72334caba85e114c076aef467e6987e1", "consensus_sequence_R2_name": "220636_S57_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3167,7 +3167,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3204,7 +3204,7 @@ "consensus_sequence_R1_name": "220637_S58_R1_001.fastq.gz", "consensus_sequence_R2_md5": "1c7c1bb51da20c0e8c9661436f598cc2", "consensus_sequence_R2_name": "220637_S58_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3223,7 +3223,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3260,7 +3260,7 @@ "consensus_sequence_R1_name": "220638_S59_R1_001.fastq.gz", "consensus_sequence_R2_md5": "d4d3b6325ef1ca17f6d36953b050f532", "consensus_sequence_R2_name": "220638_S59_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3279,7 +3279,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3316,7 +3316,7 @@ "consensus_sequence_R1_name": "220639_S60_R1_001.fastq.gz", "consensus_sequence_R2_md5": "a89de5a74985de324670f41ef730b29b", "consensus_sequence_R2_name": "220639_S60_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3335,7 +3335,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3372,7 +3372,7 @@ "consensus_sequence_R1_name": "220640_S61_R1_001.fastq.gz", "consensus_sequence_R2_md5": "40da6eac77dcd3c82f9531e3bc5f4e9c", "consensus_sequence_R2_name": "220640_S61_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3391,7 +3391,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3428,7 +3428,7 @@ "consensus_sequence_R1_name": "220642_S62_R1_001.fastq.gz", "consensus_sequence_R2_md5": "cd7a5f03488794eeec2b42e3c5dd73dd", "consensus_sequence_R2_name": "220642_S62_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3447,7 +3447,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.617.2", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3484,7 +3484,7 @@ "consensus_sequence_R1_name": "220644_S63_R1_001.fastq.gz", "consensus_sequence_R2_md5": "68173f24d15e48a74b7b46a0937a5436", "consensus_sequence_R2_name": "220644_S63_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3503,7 +3503,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3540,7 +3540,7 @@ "consensus_sequence_R1_name": "220646_S64_R1_001.fastq.gz", "consensus_sequence_R2_md5": "425f1969ebcdd626729c94668f6c9985", "consensus_sequence_R2_name": "220646_S64_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3559,7 +3559,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3596,7 +3596,7 @@ "consensus_sequence_R1_name": "220647_S65_R1_001.fastq.gz", "consensus_sequence_R2_md5": "dc234549b290f2649e7ae285aee6ff5b", "consensus_sequence_R2_name": "220647_S65_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3615,7 +3615,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3652,7 +3652,7 @@ "consensus_sequence_R1_name": "220648_S66_R1_001.fastq.gz", "consensus_sequence_R2_md5": "ca841d76f56036e00b663be25fe32313", "consensus_sequence_R2_name": "220648_S66_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3671,7 +3671,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3708,7 +3708,7 @@ "consensus_sequence_R1_name": "220649_S67_R1_001.fastq.gz", "consensus_sequence_R2_md5": "d820aca88a3637fb44bb648d9a6a03c1", "consensus_sequence_R2_name": "220649_S67_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3727,7 +3727,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3764,7 +3764,7 @@ "consensus_sequence_R1_name": "220650_S68_R1_001.fastq.gz", "consensus_sequence_R2_md5": "2b596c41ad86057f9b45c60e1e551139", "consensus_sequence_R2_name": "220650_S68_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3783,7 +3783,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3820,7 +3820,7 @@ "consensus_sequence_R1_name": "220651_S69_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f9f7118d4eacdcff059f92a352e8f832", "consensus_sequence_R2_name": "220651_S69_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3839,7 +3839,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3876,7 +3876,7 @@ "consensus_sequence_R1_name": "220652_S70_R1_001.fastq.gz", "consensus_sequence_R2_md5": "aa16ec3d36d7b457696f81ddd489340b", "consensus_sequence_R2_name": "220652_S70_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3895,7 +3895,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3932,7 +3932,7 @@ "consensus_sequence_R1_name": "220653_S71_R1_001.fastq.gz", "consensus_sequence_R2_md5": "d0613e93a129a7f935f44e9f8fe6dad7", "consensus_sequence_R2_name": "220653_S71_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -3951,7 +3951,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -3988,7 +3988,7 @@ "consensus_sequence_R1_name": "220654_S72_R1_001.fastq.gz", "consensus_sequence_R2_md5": "43eabe0ccbc64a6762f07691b6cb9b78", "consensus_sequence_R2_name": "220654_S72_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4007,7 +4007,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4044,7 +4044,7 @@ "consensus_sequence_R1_name": "220655_S73_R1_001.fastq.gz", "consensus_sequence_R2_md5": "c1c5d439d06d28839122cee8ec2a8a26", "consensus_sequence_R2_name": "220655_S73_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4063,7 +4063,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4100,7 +4100,7 @@ "consensus_sequence_R1_name": "220656_S74_R1_001.fastq.gz", "consensus_sequence_R2_md5": "d4645048ab66627ec855d1231b4207a6", "consensus_sequence_R2_name": "220656_S74_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4119,7 +4119,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4156,7 +4156,7 @@ "consensus_sequence_R1_name": "220657_S75_R1_001.fastq.gz", "consensus_sequence_R2_md5": "4de125f0f89a02caf060259ff7ba97fd", "consensus_sequence_R2_name": "220657_S75_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4175,7 +4175,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4212,7 +4212,7 @@ "consensus_sequence_R1_name": "220658_S76_R1_001.fastq.gz", "consensus_sequence_R2_md5": "b8d3fb213057c4d1f909e187789ad8f1", "consensus_sequence_R2_name": "220658_S76_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4231,7 +4231,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4268,7 +4268,7 @@ "consensus_sequence_R1_name": "220659_S77_R1_001.fastq.gz", "consensus_sequence_R2_md5": "12d26a620109b24172e517a03edca796", "consensus_sequence_R2_name": "220659_S77_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4287,7 +4287,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4324,7 +4324,7 @@ "consensus_sequence_R1_name": "220660_S78_R1_001.fastq.gz", "consensus_sequence_R2_md5": "fae8c6af23e3fac5a9a448712c4613b6", "consensus_sequence_R2_name": "220660_S78_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4343,7 +4343,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4380,7 +4380,7 @@ "consensus_sequence_R1_name": "220661_S79_R1_001.fastq.gz", "consensus_sequence_R2_md5": "00762bb19883db46289ef9047e9aa662", "consensus_sequence_R2_name": "220661_S79_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4399,7 +4399,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4436,7 +4436,7 @@ "consensus_sequence_R1_name": "220663_S80_R1_001.fastq.gz", "consensus_sequence_R2_md5": "8325daa2cb930e554c1a576ae529555b", "consensus_sequence_R2_name": "220663_S80_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4455,7 +4455,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4492,7 +4492,7 @@ "consensus_sequence_R1_name": "220664_S81_R1_001.fastq.gz", "consensus_sequence_R2_md5": "43d5cb91ffc5575a15a276c22eaf8db8", "consensus_sequence_R2_name": "220664_S81_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4511,7 +4511,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4548,7 +4548,7 @@ "consensus_sequence_R1_name": "220665_S82_R1_001.fastq.gz", "consensus_sequence_R2_md5": "a4cf0e9a3dbdefd46a928cf18acf5f08", "consensus_sequence_R2_name": "220665_S82_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4567,7 +4567,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4604,7 +4604,7 @@ "consensus_sequence_R1_name": "220666_S83_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f11417d562a870b154d8034c60cb997f", "consensus_sequence_R2_name": "220666_S83_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4623,7 +4623,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.617.2", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4660,7 +4660,7 @@ "consensus_sequence_R1_name": "220667_S84_R1_001.fastq.gz", "consensus_sequence_R2_md5": "fe3a55379689e22cf111e1287c32f45f", "consensus_sequence_R2_name": "220667_S84_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4679,7 +4679,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4716,7 +4716,7 @@ "consensus_sequence_R1_name": "220668_S85_R1_001.fastq.gz", "consensus_sequence_R2_md5": "01fc8610639039fae3a5039aa0f8ce3e", "consensus_sequence_R2_name": "220668_S85_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4735,7 +4735,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4772,7 +4772,7 @@ "consensus_sequence_R1_name": "220669_S86_R1_001.fastq.gz", "consensus_sequence_R2_md5": "866f493a5fca69d1219839e25a2c59c1", "consensus_sequence_R2_name": "220669_S86_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4791,7 +4791,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4828,7 +4828,7 @@ "consensus_sequence_R1_name": "220670_S87_R1_001.fastq.gz", "consensus_sequence_R2_md5": "2cb2bfa6bdd8d37e073ce386a51eb222", "consensus_sequence_R2_name": "220670_S87_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4847,7 +4847,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4884,7 +4884,7 @@ "consensus_sequence_R1_name": "220671_S88_R1_001.fastq.gz", "consensus_sequence_R2_md5": "63075cf1ff8543ed1f685c34f145af53", "consensus_sequence_R2_name": "220671_S88_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4903,7 +4903,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.17", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4940,7 +4940,7 @@ "consensus_sequence_R1_name": "220672_S89_R1_001.fastq.gz", "consensus_sequence_R2_md5": "9508309f8b2d201cb8fcd9a96e4592b2", "consensus_sequence_R2_name": "220672_S89_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -4959,7 +4959,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -4996,7 +4996,7 @@ "consensus_sequence_R1_name": "220675_S90_R1_001.fastq.gz", "consensus_sequence_R2_md5": "dad21b92354af748bacf678f6ad1c6a6", "consensus_sequence_R2_name": "220675_S90_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5015,7 +5015,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -5052,7 +5052,7 @@ "consensus_sequence_R1_name": "220677_S91_R1_001.fastq.gz", "consensus_sequence_R2_md5": "0bcc1af3d0663e0cfa0edfedd533155e", "consensus_sequence_R2_name": "220677_S91_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5071,7 +5071,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -5108,7 +5108,7 @@ "consensus_sequence_R1_name": "220678_S92_R1_001.fastq.gz", "consensus_sequence_R2_md5": "a2bd2aafc26b8ff21e95dfea74c4e38f", "consensus_sequence_R2_name": "220678_S92_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5127,7 +5127,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "BA.1.1.1", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -5164,7 +5164,7 @@ "consensus_sequence_R1_name": "220679_S93_R1_001.fastq.gz", "consensus_sequence_R2_md5": "f4b182052d1fb7f0690719572d5e37d3", "consensus_sequence_R2_name": "220679_S93_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5183,7 +5183,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -5220,7 +5220,7 @@ "consensus_sequence_R1_name": "220680_S94_R1_001.fastq.gz", "consensus_sequence_R2_md5": "994e273a5f941151c52727fa27732e03", "consensus_sequence_R2_name": "220680_S94_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5239,7 +5239,7 @@ "lineage_analysis_software_version": "0", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", @@ -5276,7 +5276,7 @@ "consensus_sequence_R1_name": "220684_S95_R1_001.fastq.gz", "consensus_sequence_R2_md5": "be0059af911542a8329249cc6fd4b50e", "consensus_sequence_R2_name": "220684_S95_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -5295,7 +5295,7 @@ "lineage_analysis_software_version": "0", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "Unassigned", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json index a0aa0203..45ce3775 100644 --- a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json +++ b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json @@ -12,7 +12,7 @@ "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -31,7 +31,7 @@ "lineage_analysis_software_version": "4.0.6", "lineage_identification_date": "2022-05-12 14:55:38.607792", "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "long_table_path": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/20220208", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json b/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json index 01bc3b8f..a017ca4a 100644 --- a/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json +++ b/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json @@ -54,8 +54,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "No consta", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", - "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r1_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/bioinfoshare/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", "rna_extraction_protocol": "RT-PCR", "runID": "MiSeaq_GN_195", "run_alias": "NOT_FOUND.fastq.gz", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ceed4f36..9ffe7492 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -212,6 +212,8 @@ def validate_software_mandatory_files(self, files_dict): method_name = f"{self.validate_software_mandatory_files.__name__}" missing_required = [] for key in self.software_config: + if key == "fixed_values": + continue if self.software_config[key].get("required") is True: try: files_dict[key] @@ -224,7 +226,7 @@ def validate_software_mandatory_files(self, files_dict): self.log_report.update_log_report( method_name, "error", - f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}", + f"Missing mandatory files in {self.software_name}:{', '.join(missing_required)}", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: @@ -676,7 +678,15 @@ def add_bioinfo_files_path(self, files_found_dict, j_data): file_path = file break # Exit loop if match found path_key = f"{self.software_name}_filepath_{key}" - row[path_key] = file_path + if file_path != "Not Provided [GENEPIO:0001668]": + analysis_results_path = os.path.join( + self.output_folder, + "analysis_results", + os.path.basename(file_path), + ) + row[path_key] = analysis_results_path + else: + row[path_key] = file_path if self.software_config[key].get("extract"): self.extract_file( file=file_path, diff --git a/tests/data/read_lab_metadata/metadata_lab_test.xlsx b/tests/data/read_lab_metadata/metadata_lab_test.xlsx old mode 100755 new mode 100644 index 975bdde8..9baba5b8 Binary files a/tests/data/read_lab_metadata/metadata_lab_test.xlsx and b/tests/data/read_lab_metadata/metadata_lab_test.xlsx differ diff --git a/tests/data/sftp_handle/configuration.json b/tests/data/sftp_handle/configuration.json index 33bd9cb6..9cb4f796 100755 --- a/tests/data/sftp_handle/configuration.json +++ b/tests/data/sftp_handle/configuration.json @@ -1,14 +1,26 @@ { "lab_metadata": { "fixed_fields": { - "host_disease": "COVID-19", - "tax_id": "2697049", - "organism": "Severe acute respiratory syndrome coronavirus 2", "study_type": "Whole Genome Sequencing", "collector_name": "Not Provided" }, + "organism_mapping": { + "Severe acute respiratory syndrome coronavirus 2 [LOINC:LA31065-8]": { + "tax_id": "2697049", + "host_disease": "COVID-19 [SNOMED:840539006]" + }, + "Respiratory syncytial virus [SNOMED:6415009]": { + "tax_id": "1281", + "host_disease": "Respiratory Syncytial Virus Infection [SNOMED:55735004]" + }, + "Influenza virus [SNOMED:725894000]": { + "tax_id": "11320", + "host_disease": "Influenza Infection [SNOMED:408687004]" + } + }, "metadata_lab_heading": [ - "Public Health sample id (SIVIES)", + "Organism", + "Public Health sample id (SIVIRA)", "Sample ID given by originating laboratory", "Sample ID given by the submitting laboratory", "Sample ID given in the microbiology lab", @@ -29,7 +41,8 @@ "Environmental System", "Collection Device", "Host", - "Host Age", + "Host Age Years", + "Host Age Months", "Host Gender", "Sequencing Date", "Nucleic acid extraction protocol", @@ -54,8 +67,36 @@ "Diagnostic Pcr Ct Value-2", "Authors", "Sequence file R1 fastq", - "Sequence file R2 fastq" + "Sequence file R2 fastq", + "Vaccinated", + "Specific medication for treatment or prophylaxis", + "Hospitalization", + "Admission to intensive care unit", + "Death", + "Immunosuppression" ], + "alt_heading_equivalences": { + "Sample ID": "Sample ID given for sequencing", + "LAB ID" : "Originating Laboratory", + "Sequencing date\n Formato: YYYY-MM-DD" : "Sequencing Date", + "Commercial All-in-one library kit" : "Commercial All-in-one library kit", + "Library preparation kit " : "Library Preparation Kit", + "Enrichment protocol" : "Enrichment Protocol", + "if enrichment protocol is Other, specify" : "If Enrichment Protocol Is Other, Specify", + "Amplicon protocol" : "Enrichment panel/assay", + "if enrichment panel/assay is Other, specify" : "If Enrichment panel/assay Is Other, Specify", + "Amplicon version" : "Enrichment panel/assay version", + "Number Of Samples In Run" : "Number Of Samples In Run", + "Number of variants with effect (missense, frameshit, stop codon)" : "Number of variants with effect", + "Sequencing platforms (Illumina, Nanopore, IonTorrent, PacBio, other)" : "Sequencing Instrument Model", + "Variant designation table filename" : "Lineage analysis file", + "Library preparation kit" : "Library Preparation Kit", + "Library layout" : "Library Layout", + "Read lenght" : "Read length", + "SARS-CoV-2 Lineage designation" : "Lineage designation", + "fastq filename R1" : "Sequence file R1 fastq", + "fastq filename R2" : "Sequence file R2 fastq" + }, "lab_metadata_req_json": { "laboratory_data": { "file": "laboratory_address.json", @@ -204,8 +245,12 @@ "sftp_port": "22" }, "metadata_processing": { + "sample_id_col": "Sample ID given for sequencing", "header_flag": "CAMPO", - "excel_sheet": "METADATA_LAB" + "excel_sheet": "METADATA_LAB", + "alternative_sheet": "5.Viral Characterisation and Se", + "alternative_flag": "CAMPO", + "alternative_sample_id_col": "Sample ID given for sequencing" }, "abort_if_md5_mismatch": "False", "platform_storage_folder": "/tmp/relecov", @@ -215,7 +260,10 @@ ".fq", ".fq.gz", ".fasta", - ".fasta.gz" + ".fasta.gz", + ".fa", + ".fa.gz", + "bam" ], "allowed_download_options": [ "download_only", @@ -231,145 +279,55 @@ "GISAID_configuration": { "submitter": "GISAID_ID" }, - "external_url": { - "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", - "url": "/wetlab/api/", - "store_samples": "createSampleData", - "url_project_fields": "sampleProjectFields", - "url_sample_fields": "sampleFields", - "param_sample_project": "project", - "project_name": "relecov", - "token": "" - }, - "relecov": { - "server": "http://relecov-platform.isciiides.es", - "url": "/api/", + "upload_database": { + "platform":{ + "iskylims": { + "server_url": "http://relecov-iskylims.isciiides.es", + "api_url": "/wetlab/api/", + "store_samples": "create-sample", + "url_project_fields": "projects-fields", + "url_sample_fields": "sample-fields", + "param_sample_project": "project", + "project_name": "relecov", + "token": "" + }, + "relecov": { + "server_url": "http://relecov-platform.isciiides.es", + "api_url": "/api/", "store_samples": "createSampleData", "bioinfodata": "createBioinfoData", "variantdata": "createVariantData", "sftp_info": "sftpInfo", "token": "" - } - }, - "iskylims_fixed_values": { - "patientCore": "", - "sampleProject": "Relecov", - "onlyRecorded": "Yes", - "sampleLocation": "Not defined" - }, - "relecov_sample_metadata": [ - "authors", - "collecting_institution", - "collecting_lab_sample_id", - "ena_broker_name", - "ena_sample_accession", - "gisaid_accession_id", - "gisaid_virus_name", - "microbiology_lab_sample_id", - "r1_fastq_filepath", - "r2_fastq_filepath", - "schema_name", - "schema_version", - "sequencing_date", - "sequence_file_R1_md5", - "sequence_file_R2_md5", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", - "sequencing_sample_id", - "submitting_lab_sample_id" - ], - "bioinfo_analysis": { - "fixed_values": { - "assembly": "Not Provided [GENEPIO:0001668]", - "assembly_params": "Not Provided [GENEPIO:0001668]", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "commercial_open_source_both": "Open Source", - "consensus_params": "-p vcf -f", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "depth_of_coverage_threshold": ">10x", - "if_assembly_other": "Not Provided [GENEPIO:0001668]", - "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", - "if_consensus_other": "Not Provided [GENEPIO:0001668]", - "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]", - "if_mapping_other": "Not Provided [GENEPIO:0001668]", - "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", - "lineage_analysis_software_name": "pangolin", - "mapping_params": "--seed 1", - "mapping_software_name": "BOWTIE2_ALIGN", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "preprocessing_software_name": "FASTP", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "variant_calling_software_name": "IVAR_VARIANTS" - }, - "feed_empty_fields":{ - "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", - "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" - }, - "required_file": { - "variants_metrics": "summary_variants_metrics_mqc.csv", - "versions": "software_versions.yml", - "mapping_stats": "mapping_illumina_stats.tab" - }, - "mapping_consensus": [ - "consensus_genome_length", - "consensus_sequence_filename", - "consensus_sequence_filepath", - "consensus_sequence_md5", - "number_of_base_pairs_sequenced" - ], - "mapping_pangolin": { - "variant_name": "scorpio_call", - "lineage_name": "lineage", - "lineage_algorithm_software_version": "version", - "lineage_analysis_software_version": "pangolin_version", - "lineage_analysis_scorpio_version": "scorpio_version", - "lineage_analysis_constellation_version": "constellation_version" - }, - "mapping_stats": { - "analysis_date": "analysis_date", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_Ns": "%Ns10x", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "qc_filtered": "totalreads", - "reference_genome_accession": "Virussequence", - "read_length": "read_length" - }, - "mapping_variant_metrics": { - "ns_per_100_kbp": "# Ns per 100kb consensus" - }, - "mapping_version": { - "bioinformatics_protocol_software_version": { - "Workflow": "nf-core/viralrecon" - }, - "consensus_sequence_software_version": { - "BCFTOOLS_CONSENSUS": "bcftools" - }, - "dehosting_method_software_version": { - "KRAKEN2_KRAKEN2": "kraken2" - }, - "mapping_software_version": { - "BOWTIE2_ALIGN": "bowtie2" - }, - "preprocessing_software_version": { - "FASTP": "fastp" - }, - "variant_calling_software_version": { - "IVAR_VARIANTS": "ivar" } }, - "required_fields_from_lab_json": { - "read_length": "number_of_base_pairs_sequenced", - "schema_name": "schema_name", - "schema_version": "schema_version", - "sequencing_sample_id": "sequencing_sample_id" - } + "iskylims_fixed_values": { + "patient_core": "", + "sample_project": "Relecov", + "only_recorded": "Yes", + "sample_location": "Not defined" + }, + "relecov_sample_metadata": [ + "authors", + "collecting_institution", + "collecting_lab_sample_id", + "ena_broker_name", + "ena_sample_accession", + "gisaid_accession_id", + "gisaid_virus_name", + "microbiology_lab_sample_id", + "r1_fastq_filepath", + "r2_fastq_filepath", + "schema_name", + "schema_version", + "sequencing_date", + "sequence_file_R1_md5", + "sequence_file_R2_md5", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "sequencing_sample_id", + "submitting_lab_sample_id" + ] }, "ENA_fields": { "ENA_configuration": { @@ -492,5 +450,49 @@ "fastq_r2_md5" ] } + }, + "pipeline_manager": { + "analysis_group": "RLV", + "analysis_user": "icasas_C", + "doc_folder": "DOC", + "analysis_folder": "ANALYSIS", + "sample_stored_folder": "RAW", + "sample_link_folder": "00-reads", + "organism_config": { + "Severe acute respiratory syndrome coronavirus 2 [LOINC:LA31065-8]": { + "pipeline_template": "viralrecon", + "service_tag": "SARSCOV2", + "group_by_fields": [ + "sequencing_instrument_platform", + "enrichment_panel", + "enrichment_panel_version" + ] + }, + "Respiratory syncytial virus [SNOMED:6415009]": { + "pipeline_template": "IRMA", + "service_tag": "GENOMERSV", + "group_by_fields": [ + "sequencing_instrument_platform", + "enrichment_panel", + "enrichment_panel_version" + ] + }, + "Influenza virus [SNOMED:725894000]": { + "pipeline_template": "IRMA", + "service_tag": "GENOMEFLU", + "group_by_fields": [ + "sequencing_instrument_platform" + ] + } + } + }, + "mail_sender":{ + "delivery_template_path_file": "./relecov_tools/templates/", + "email_host": "mx2.isciii.es", + "email_port": "587", + "email_host_user": "bioinformatica@isciii.es", + "email_use_tls": "True", + "yaml_cred_path": "~/buisciii_config.yml", + "institutions_guide_path": "/data/bioinfoshare/UCCT_Relecov/statics/institutions_guide.json" } } diff --git a/tests/data/sftp_handle/datatest1/metadata_validation_test.xlsx b/tests/data/sftp_handle/datatest1/metadata_validation_test.xlsx deleted file mode 100755 index 02e3c8ba..00000000 Binary files a/tests/data/sftp_handle/datatest1/metadata_validation_test.xlsx and /dev/null differ diff --git a/tests/data/sftp_handle/datatest1/metadata_validation_test_dataset1.xlsx b/tests/data/sftp_handle/datatest1/metadata_validation_test_dataset1.xlsx new file mode 100644 index 00000000..39535191 Binary files /dev/null and b/tests/data/sftp_handle/datatest1/metadata_validation_test_dataset1.xlsx differ diff --git a/tests/data/sftp_handle/datatest2/metadata_validation_test_dataset2.xlsx b/tests/data/sftp_handle/datatest2/metadata_validation_test_dataset2.xlsx new file mode 100644 index 00000000..d2f84cce Binary files /dev/null and b/tests/data/sftp_handle/datatest2/metadata_validation_test_dataset2.xlsx differ diff --git a/tests/data/sftp_handle/datatest2/test2_metadata_template_v2.0.1.xlsx b/tests/data/sftp_handle/datatest2/test2_metadata_template_v2.0.1.xlsx deleted file mode 100644 index e7192458..00000000 Binary files a/tests/data/sftp_handle/datatest2/test2_metadata_template_v2.0.1.xlsx and /dev/null differ diff --git a/tests/test_wrapper_handle.py b/tests/test_wrapper_handle.py index 2ff8b879..4398e02b 100755 --- a/tests/test_wrapper_handle.py +++ b/tests/test_wrapper_handle.py @@ -24,6 +24,7 @@ def main(): "download_option": args.download_option, "output_location": os.environ["OUTPUT_LOCATION"], "target_folders": args.target_folders, + "sftp_port": os.environ["TEST_PORT"], } prepare_remote_test(**val_dict) @@ -106,32 +107,31 @@ def prepare_remote_test(**kwargs): download_manager.relecov_sftp.close_connection() print("Create Intermediate YML") - conf_file = generate_config_yaml( + conf_file = generate_config_yaml( # Generate the YAML config file kwargs["download_option"], kwargs["target_folders"], ) print("Initiating ProcessWrapper") - wrapper_manager = ProcessWrapper( + wrapper_manager = ProcessWrapper( # Initialize ProcessWrapper with the config file config_file=conf_file, output_folder=kwargs["output_location"], ) print("Update Wrapper params") - wrapper_manager.download_params = { + wrapper_manager.download_params = { # Set download parameters "user": os.environ["TEST_USER"], "passwd": os.environ["TEST_PASSWORD"], "download_option": kwargs["download_option"], "output_location": kwargs["output_location"], "target_folders": kwargs["target_folders"], + "sftp_port": kwargs["sftp_port"], } - wrapper_manager.download_manager.relecov_sftp.sftp_port = os.environ["TEST_PORT"] - def test_wrapper(wrapper_manager): - wrapper_manager.run_wrapper() + wrapper_manager.run_wrapper() # Execute the wrapper process - test_wrapper(wrapper_manager) + test_wrapper(wrapper_manager) # Run the wrapper function if __name__ == "__main__":