Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
This PR adds an optional input (trimmomatic_args) to the trimmomatic and trimmomatic_se tasks (tasks/task_read_clean.wdl) so that additional arguments can be appended to the trimmomatic command.
For example, providing "phred33" for this input will specify that Phred33 is the quality encoding for the sequencing data to be analyzed. By default, no arguments are provided.
This PR also adds this input to workflows/wf_read_QC_trim.wdl and workflows/wf_read_QC_trim_se.wdl
This PR adds an optional input (trimmomatic_args) to the trimmomatic and trimmomatic_se tasks (tasks/task_read_clean.wdl) so that additional arguments can be appended to the trimmomatic command.
For example, providing "phred33" for this input will specify that Phred33 is the quality encoding for the sequencing data to be analyzed. By default, no arguments are provided.
This PR also adds this input to workflows/wf_read_QC_trim.wdl and workflows/wf_read_QC_trim_se.wdl
This PR also adds a task for running fastp (https://github.com/OpenGene/fastp), but does not incorporate it into any workflows
This branch has been tested on:
10 samples with "-phred33" added as an optional input https://console.cloud.google.com/storage/browser/fc-1162d2b8-109d-42a8-b1b0-c05141aa98ad/submissions/afd161e2-2a36-400a-aa5b-7ff2382b693b?authuser=michelle.scribner@theiagen.com
10 samples with no optional input provided to verify that previous results are unchanged https://console.cloud.google.com/storage/browser/fc-1162d2b8-109d-42a8-b1b0-c05141aa98ad/submissions/202e20d6-04d8-4cdf-8c46-caf25cf08ea1?authuser=michelle.scribner@theiagen.com