metapool + wallclock time updates (#70)

* Prep-info file generation/Replicate tests added. * Updated source of prep-info filepaths. * Updated load_preps_into_qiita() to support replicates * Added replicates tests. * Updates based on feedback * Updates based on feedback * wallclock_time_in_hours -> wallclock_time_in_minutes * removed obsolete msg * sample sample-sheets updated to latest metapool spec * Updated sample-sheet
qiita-spots · Sep 5, 2023 · 58c509d · 58c509d
1 parent 6a3b503
commit 58c509d
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Showing 6 changed files with 1,264 additions and 1,265 deletions.
diff --git a/qp_klp/Step.py b/qp_klp/Step.py
@@ -247,7 +247,7 @@ def _convert_bcl_to_fastq(self, config, input_file_path):
                                  config['queue'],
                                  config['nodes'],
                                  config['nprocs'],
-                                 config['wallclock_time_in_hours'],
+                                 config['wallclock_time_in_minutes'],
                                  config['per_process_memory_limit'],
                                  config['executable_path'],
                                  config['modules_to_load'],
@@ -266,7 +266,7 @@ def _quality_control(self, config, input_file_path):
                        config['queue'],
                        config['nodes'],
                        config['nprocs'],
-                       config['wallclock_time_in_hours'],
+                       config['wallclock_time_in_minutes'],
                        config['job_total_memory_limit'],
                        config['fastp_executable_path'],
                        config['minimap2_executable_path'],
@@ -294,7 +294,7 @@ def _generate_reports(self):
                                self.master_qiita_job_id,
                                config['queue'],
                                config['nodes'],
-                               config['wallclock_time_in_hours'],
+                               config['wallclock_time_in_minutes'],
                                config['job_total_memory_limit'],
                                self.job_pool_size,
                                config['multiqc_config_file_path'],

diff --git a/qp_klp/tests/data/another-good-sample-sheet.csv b/qp_klp/tests/data/another-good-sample-sheet.csv
@@ -1,35 +1,35 @@
-[Header],,,,,,,,,,
-IEMFileVersion,4,,,,,,,,,
-Investigator Name,Knight,,,,,,,,,
-Experiment Name,RKL0042,,,,,,,,,
-Date,2020-02-26,,,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,,,
-Application,FASTQ Only,,,,,,,,,
-Assay,Metagenomic,,,,,,,,,
-Description,,,,,,,,,,
-Chemistry,Default,,,,,,,,,
-,,,,,,,,,,
-[Reads],,,,,,,,,,
-150,,,,,,,,,,
-150,,,,,,,,,,
-,,,,,,,,,,
-[Settings],,,,,,,,,,
-ReverseComplement,0,,,,,,,,,
-,,,,,,,,,,
-[Data],,,,,,,,,,
-Lane,Sample_ID,Sample_Name,Sample_Plate,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Well_description
-1,AAAAA_AAAAAA,1234567890a,TestProject_99999_P40,A1,iTru7_107_07,CCGACTAT,iTru5_01_A,ACCGACAA,TestProject_99999,text_description
-1,BBBBB_BBBBBB,234567890ab,TestProject_99999_P40,C1,iTru7_107_08,CCGACTAT,iTru5_02_A,CTTCGCAA,TestProject_99999,text_description
-1,CCCCC_CCCCCC,034567890abc,TestProject_99999_P40,E1,iTru7_107_09,GCCTTGTT,iTru5_03_A,AACACCAC,TestProject_99999,a registered tube-id, with a leading zero
-1,DDDDD_DDDDDD,4567890abcd,TestProject_99999_P40,E1,iTru7_107_09,GGGGGGGG,iTru5_03_A,TTTTTTTT,TestProject_99999,a truly unregistered tube-id
-1,BLANK1_1BCD,BLANK1.1BCD,TestProject_99999_P40,M23,iTru7_201_05,AGAATGCC,iTru5_11_H,GCGTTAGA,TestProject_99999,text_description
-1,BLANK_UNREG,BLANK_UNREG,TestProject_99999_P40,M23,iTru7_201_05,AAAAAAAA,iTru5_11_H,CCCCCCCC,TestProject_99999,unregistered blank
-,,,,,,,,,,
-[Bioinformatics],,,,,,,,,,
-Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,
-TestProject_99999,99999,False,AACC,GGTT,False,Nextera,Equipment,,,
-,,,,,,,,,,
-[Contact],,,,,,,,,,
-Email,Sample_Project,,,,,,,,,
-test@lol.com,TestProject_99999,,,,,,,,,
-,,,,,,,,,,
+[Header],,,,,,,,,,,
+IEMFileVersion,4,,,,,,,,,,
+Investigator Name,Knight,,,,,,,,,,
+Experiment Name,RKL0042,,,,,,,,,,
+Date,2020-02-26,,,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,,,
+Application,FASTQ Only,,,,,,,,,,
+Assay,Metagenomic,,,,,,,,,,
+Description,,,,,,,,,,,
+Chemistry,Default,,,,,,,,,,
+,,,,,,,,,,,
+[Reads],,,,,,,,,,,
+150,,,,,,,,,,,
+150,,,,,,,,,,,
+,,,,,,,,,,,
+[Settings],,,,,,,,,,,
+ReverseComplement,0,,,,,,,,,,
+,,,,,,,,,,,
+[Data],,,,,,,,,,,
+Lane,Sample_ID,Sample_Name,Sample_Plate,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,syndna_pool_number,Well_description
+1,AAAAA_AAAAAA,1234567890a,TestProject_99999_P40,A1,iTru7_107_07,CCGACTAT,iTru5_01_A,ACCGACAA,TestProject_99999,pool1,text_description
+1,BBBBB_BBBBBB,234567890ab,TestProject_99999_P40,C1,iTru7_107_08,CCGACTAT,iTru5_02_A,CTTCGCAA,TestProject_99999,pool2,text_description
+1,CCCCC_CCCCCC,034567890abc,TestProject_99999_P40,E1,iTru7_107_09,GCCTTGTT,iTru5_03_A,AACACCAC,TestProject_99999,pool1,a registered tube-id, with a leading zero
+1,DDDDD_DDDDDD,4567890abcd,TestProject_99999_P40,E1,iTru7_107_09,GGGGGGGG,iTru5_03_A,TTTTTTTT,TestProject_99999,pool2,a truly unregistered tube-id
+1,BLANK1_1BCD,BLANK1.1BCD,TestProject_99999_P40,M23,iTru7_201_05,AGAATGCC,iTru5_11_H,GCGTTAGA,TestProject_99999,pool1,text_description
+1,BLANK_UNREG,BLANK_UNREG,TestProject_99999_P40,M23,iTru7_201_05,AAAAAAAA,iTru5_11_H,CCCCCCCC,TestProject_99999,pool2,unregistered blank
+,,,,,,,,,,,
+[Bioinformatics],,,,,,,,,,,
+Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,
+TestProject_99999,99999,False,AACC,GGTT,False,Nextera,Equipment,,,,
+,,,,,,,,,,,
+[Contact],,,,,,,,,,,
+Email,Sample_Project,,,,,,,,,,
+test@lol.com,TestProject_99999,,,,,,,,,,
+,,,,,,,,,,,