nf-vectra-to-htan

This workflow takes qptiff files from Vectra miF images and outputs OME-TIFF images suitable for submission to the HTAN DCC with the Imaging Level 2 template.

It performs the following steps

• Converts the first series in the qptiff (the full resolution image) to OME-TIFF via bioformats2raw and raw2ometiff. Other images included in the qptiff (the thumbnail, overview and label) are discarded.
• Removes AcquisitionDate and StructuredAnnotations from the OME-XML
• Removes DateTime from the TIFF tags.

It outputs a tiled, pyramidal, single scene OME-TIFF file.

Requirements

• NextFlow
• Docker

Usage

nextflow run ncihtan/nf-vectra-to-htan --input <path-to-samplesheet>

Inputs

Create a CSV samplesheet containing one column called image. for example:

image
path/to/myimage.qptiff
s3://mybucket/myimage.qptiff

Outputs

By default this outputs into a new directory called outputs in your current working directory.

Parameters

• outdir: Directory for outputs (default: "outputs")
• suffix: Suffix for output files (default: "_htan")

Docker images

This workflow uses two existing Docker images that support other HTAN pipelines

• nf-artist: This image is used for the conversion step
• nf-imagecleaner: This image is used for the deidentification steps