diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7d09207 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.DS_Store +.nextflow* +work/ +outputs/ +data/ +test_samplesheet.csv diff --git a/README.md b/README.md index ac54b0f..89307bd 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,44 @@ # nf-vectra-to-htan - A NextFlow workflow to prepare Vectra mIF qptiff files for the HTAN DCC + +A NextFlow workflow to prepare Vectra mIF qptiff files for the HTAN DCC. + +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](https://nextflow.io/) +- [Docker](https://docs.docker.com/engine/install/) + +### Usage + +``` +nextflow run ncihtan/nf-vectra-to-htan --input +``` + +### 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`") \ No newline at end of file diff --git a/bin/clean_ometiff.py b/bin/clean_ometiff.py new file mode 100755 index 0000000..e06f3d2 --- /dev/null +++ b/bin/clean_ometiff.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python + +import sys +import tifftools +import ome_types +import os + +input = sys.argv[1] + + +def split_all_ext(filename): + basename = filename + extensions = [] + while "." in basename: + basename, ext = os.path.splitext(basename) + extensions.append(ext) + return basename, "".join(reversed(extensions)) + + +insert_string = "_cleaned" + +basename, all_ext = split_all_ext(input) + +new_filename = f"{basename}{insert_string}{all_ext}" +print(new_filename) + +ome = ome_types.from_tiff(input) +ome.structured_annotations.clear() +for i, exp in enumerate(ome.experimenters): + ome.experimenters[i].email = None + ome.experimenters[i].first_name = None + ome.experimenters[i].last_name = None +for i, img in enumerate(ome.images): + ome.images[i].acquisition_date = None + +set_list = [(tifftools.Tag.IMAGEDESCRIPTION, ome_types.to_xml(ome))] + +tifftools.tiff_set(input, overwrite=True, setlist=set_list) diff --git a/bin/clean_tiff.py b/bin/clean_tiff.py new file mode 100755 index 0000000..f777b61 --- /dev/null +++ b/bin/clean_tiff.py @@ -0,0 +1,41 @@ +#!/usr/bin/env python + +import argparse +import tifftools +import os + +import argparse + +parser = argparse.ArgumentParser() + +parser.add_argument("input") +parser.add_argument("--suffix", default="_cleaned") + +args = parser.parse_args() + + +def split_all_ext(filename): + basename = filename + extensions = [] + while "." in basename: + basename, ext = os.path.splitext(basename) + extensions.append(ext) + return basename, "".join(reversed(extensions)) + + +basename, all_ext = split_all_ext(args.input) + +new_filename = f"{basename}{args.suffix}{all_ext}" +print(new_filename) + + +unset_list = [ + "DateTime", +] + +tifftools.tiff_set( + args.input, + output=new_filename, + overwrite=False, + unset=unset_list +) diff --git a/dump.txt b/dump.txt new file mode 100644 index 0000000..7cb777a --- /dev/null +++ b/dump.txt @@ -0,0 +1,1205 @@ +-- 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(0x3)) + Software 305 (0x131) ASCII: OME Bio-Formats 6.13.0 + TileWidth 322 (0x142) SHORT: 240 + TileLength 323 (0x143) SHORT: 240 + TileOffsets 324 (0x144) LONG8: 1894893403 + TileByteCounts 325 (0x145) LONG8: 26295 + SampleFormat 339 (0x153) SHORT: 1 (uint 1 (0x1)) diff --git a/main.nf b/main.nf new file mode 100644 index 0000000..daa50bb --- /dev/null +++ b/main.nf @@ -0,0 +1,43 @@ +#!/usr/bin/env nextflow +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + ncihtan/nf-vectra-to-htan +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Github : https://ncihtan/nf-vectra-to-htan +---------------------------------------------------------------------------------------- +*/ + +nextflow.enable.dsl = 2 + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + WORKFLOW PARAMETER VALUES +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +params.outdir = 'outputs' // Directory for outputs +params.suffix = '_htan' // Suffix for processed files + +if (params.input) { + params.input = file(params.input) + } else { + exit 1, 'Input samplesheet not specified!' + } + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + NAMED WORKFLOWS FOR PIPELINE +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { VECTRA2HTAN } from './workflows/vectra2htan.nf' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow { + VECTRA2HTAN () +} diff --git a/modules/clean_ome.nf b/modules/clean_ome.nf new file mode 100644 index 0000000..7ffafd3 --- /dev/null +++ b/modules/clean_ome.nf @@ -0,0 +1,15 @@ +process clean_ome { + container = 'ghcr.io/ncihtan/nf-imagecleaner' + input: + tuple val(meta), file(image) + output: + tuple val(meta), file(image) + stub: + """ + touch image_cleaned.ome.tiff + """ + script: + """ + clean_ometiff.py $image + """ +} diff --git a/modules/clean_tiff.nf b/modules/clean_tiff.nf new file mode 100644 index 0000000..37554a5 --- /dev/null +++ b/modules/clean_tiff.nf @@ -0,0 +1,15 @@ +process clean_tiff { + container 'ghcr.io/ncihtan/nf-imagecleaner' + input: + tuple val(meta), file(image) + output: + tuple val(meta), file('*.ome.tiff') + publishDir "$params.outdir/", mode: 'copy', overwrite: true + """ + touch image_cleaned.ome.tiff + """ + script: + """ + clean_tiff.py $image --suffix $params.suffix + """ +} diff --git a/modules/qptiff2ometiff.nf b/modules/qptiff2ometiff.nf new file mode 100644 index 0000000..8ec12b0 --- /dev/null +++ b/modules/qptiff2ometiff.nf @@ -0,0 +1,19 @@ +process QPTIFF2OMETIFF { + tag {"$meta.id"} + label "process_medium" + container 'ghcr.io/sage-bionetworks-workflows/nf-artist:latest' + input: + tuple val(meta), file(image) + output: + tuple val(meta), file("${image.simpleName}.ome.tiff") + stub: + """ + touch raw_dir + touch "${image.simpleName}.ome.tiff" + """ + script: + """ + bioformats2raw $image 'raw_dir' -s 0 + raw2ometiff 'raw_dir' "${image.simpleName}.ome.tiff" + """ +} diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000..41c0138 --- /dev/null +++ b/nextflow.config @@ -0,0 +1,37 @@ +// nextflow.config + +docker.enabled = true + +profiles { + test { includeConfig 'conf/test.config'} + sage { includeConfig 'conf/sage.config'} + tower { + process { + cpus = {1 * task.attempt} + memory = {2.GB * task.attempt} + maxRetries = 3 + errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore' } + withLabel: process_low { + cpus = {1 * task.attempt} + memory = {2.GB * task.attempt} + maxRetries = 3 + errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore' } + } + withLabel: process_medium { + cpus = {4 * task.attempt} + memory = {8.GB * task.attempt} + maxRetries = 3 + errorStrategy = {task.attempt <= 3 ? 'retry' : 'ignore' } + } + withLabel: process_high { + cpus = {8 * task.attempt} + memory = {16.GB * task.attempt} + maxRetries = 3 + errorStrategy = {task.attempt <= 3 ? 'retry' : 'ignore' } + } + } + } +} + + + diff --git a/subworkflows/convert.nf b/subworkflows/convert.nf new file mode 100644 index 0000000..38888a3 --- /dev/null +++ b/subworkflows/convert.nf @@ -0,0 +1,14 @@ +include { QPTIFF2OMETIFF } from '../modules/qptiff2ometiff.nf' + +workflow CONVERT { + take: images + + main: + + QPTIFF2OMETIFF( images ) + + QPTIFF2OMETIFF.out + .set { converted } + + emit: converted +} diff --git a/subworkflows/deid.nf b/subworkflows/deid.nf new file mode 100644 index 0000000..604ea48 --- /dev/null +++ b/subworkflows/deid.nf @@ -0,0 +1,15 @@ +include { clean_ome } from "../modules/clean_ome.nf" +include { clean_tiff } from "../modules/clean_tiff.nf" + + +workflow DEID { + take: + images + + main: + + images | clean_ome | clean_tiff | set { cleaned } + + emit: + cleaned +} diff --git a/subworkflows/samplesheet_split.nf b/subworkflows/samplesheet_split.nf new file mode 100644 index 0000000..0e2797b --- /dev/null +++ b/subworkflows/samplesheet_split.nf @@ -0,0 +1,24 @@ +workflow SAMPLESHEET_SPLIT { + take: + samplesheet + main: + Channel + .fromPath(samplesheet) + .splitCsv (header:true, sep:',' ) + // Make meta map from the samplesheet + .map { + row -> + def meta = [:] + if (row.id ) { + meta.id = row.id + } else { + meta.id = file(row.image).simpleName + } + image = file(row.image) + [meta, image] + } + .set {images } + + emit: + images +} diff --git a/workflows/vectra2htan.nf b/workflows/vectra2htan.nf new file mode 100644 index 0000000..85514d6 --- /dev/null +++ b/workflows/vectra2htan.nf @@ -0,0 +1,12 @@ +include { SAMPLESHEET_SPLIT } from '../subworkflows/samplesheet_split.nf' +include { CONVERT } from '../subworkflows/convert.nf' +// include { GET_METADATA } from '../subworkflows/get_metadata.nf' +include { DEID } from '../subworkflows/deid.nf' + +workflow VECTRA2HTAN { + SAMPLESHEET_SPLIT ( params.input ) + CONVERT( SAMPLESHEET_SPLIT.out.images ) + CONVERT.out.converted.set{converted} + // GET_METADATA( converted ) + DEID( converted ) +}