Also reverts back to the values used in the 1.0 release of PHBG in the read_QC_trim_se workflow
This PR also reorders the inputs in the read_QC_trim wf, read_QC_trim_se wf, trimmomatic task, and fastp task for consistency and to reflect the order of operations used by trimmomatic and fastp
This PR:
Reverts the trimmomatic default read trimming and filtering parameters back to the values used in the 1.0 release of PHBG in the trimmomatic task and the read_QC_trim workflow. These values were changed in https://github.com/theiagen/public_health_bacterial_genomics/pull/169
Also reverts back to the values used in the 1.0 release of PHBG in the read_QC_trim_se workflow
This PR also reorders the inputs in the read_QC_trim wf, read_QC_trim_se wf, trimmomatic task, and fastp task for consistency and to reflect the order of operations used by trimmomatic and fastp
Testing
This branch has been tested: https://console.cloud.google.com/storage/browser/fc-1162d2b8-109d-42a8-b1b0-c05141aa98ad/submissions/cd7fab66-3f17-4795-b492-647afd3e2c3d?authuser=michelle.scribner@theiagen.com
The number of reads passing filtering were confirmed to match those from v1.0 of TheiaProk
theiaprok v1.0 | num_reads_clean_pairs | num_reads_raw_pairs -- | -- | -- sample_01 | 1409757 | 1488671 sample_02 | 1255890 | 1308480 sample_03 | 601271 | 776657 sample_04 | 1780521 | 1884728 sample_05 | 542521 | 559802 | | entity:revert_trim_v1_1_id | num_reads_clean_pairs | num_reads_raw_pairs sample_01 | 1409757 | 1488671 sample_02 | 1255890 | 1308480 sample_03 | 601271 | 776657 sample_04 | 1780521 | 1884728 sample_05 | 542521 | 559802