Gathers required files and creates file containing urls to allow file download within CUH & the LGLs.
snv_path
[optional]: List of absolute paths to folder containing the variant reports for small variantscnv_path
[optional]: List of absolute paths to folder containing the variant reports for CNVsurl_duration
[optional]: Time (in seconds) until the generated links expire. (Default = 4838400)bed_file
[optional]: Static capture bed fileqc_status
[optional]: Input of xlsx file containing agreed QC status for samples in the runmultiqc_report
[optional]: Input of the MultiQC report - if not provided, will search for a MultiQC job in the project to find thislock_cells
[optional]: Determines whether to protect any populated cells in the output .xlsx from editing (Default=True)
Given a list of paths the app finds the appropriate files needed to share with the scientists by backwards searching through the file metadata for the jobs they were created from and extracting desired files. Current files outputted are:
- Run level file URLs:
- MultiQC Report
html
- QC Status Report
xlsx
- MultiQC Report
- For small variant analysis, DNAnexus URLs for:
- Variant Report
xlsx
- Coverage Report
html
- Alignment
bam
- Alignment index
bai
- Variant Report
- For copy number variant analysis, DNAnexus URLs for:
- CNV variant report
xlsx
- CNV calls for IGV
seg
- CNV visualisation
bed
- CNV target regions
bed
- Alignment
bam
- Alignment index
bai
- CNV variant report
url file
: File contained URLs for the files described above
- This app works specifically with the output of the dias pipeline, specifically expecting the path inputs to be in specific format to identify the MultiQC reports.
- Please note although both paths are optional, if none are given the app will fail