diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 491939ec..b1f66160 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,11 +49,11 @@ jobs: if: ${{ !env.MATCHED_FILES }} run: | docker pull qbicpipelines/rtarootseg:dev - docker tag qbicpipelines/rtarootseg:dev qbicpipelines/rtarootseg:dev + docker tag qbicpipelines/rtarootseg:dev qbicpipelines/rtarootseg:1.0.0 docker pull qbicpipelines/rtaratioconv:dev - docker tag qbicpipelines/rtaratioconv:dev qbicpipelines/rtaratioconv:dev + docker tag qbicpipelines/rtaratioconv:dev qbicpipelines/rtaratioconv:1.0.0 docker pull qbicpipelines/rtastat:dev - docker tag qbicpipelines/rtastat:dev qbicpipelines/rtastat:dev + docker tag qbicpipelines/rtastat:dev qbicpipelines/rtastat:1.0.0 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/push_dockerhub_ratioconv_release.yml b/.github/workflows/push_dockerhub_ratioconv_release.yml index 879cd17b..4e5439c3 100644 --- a/.github/workflows/push_dockerhub_ratioconv_release.yml +++ b/.github/workflows/push_dockerhub_ratioconv_release.yml @@ -1,4 +1,4 @@ -name: Docker push for ratioconv container (dev) +name: Docker push for ratioconv container (release) # This builds the docker image and pushes to DockerHub on: @@ -7,7 +7,7 @@ on: jobs: push_dockerhub: - name: Push new docker image to DockerHub (dev) + name: Push new docker image to DockerHub (release) runs-on: ubuntu-latest # Only run for the nf-core repo, for releases and merged PRs if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }} @@ -19,9 +19,9 @@ jobs: uses: actions/checkout@v2 - name: Build new docker image - run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtaratioconv:dev + run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtaratioconv:latest - - name: Push docker image to DockerHub (dev) + - name: Push docker image to DockerHub (release) run: | echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin docker push qbicpipelines/rtaratioconv:latest diff --git a/.github/workflows/push_dockerhub_rootseg_release.yml b/.github/workflows/push_dockerhub_rootseg_release.yml index 4fbae4cd..55932e31 100644 --- a/.github/workflows/push_dockerhub_rootseg_release.yml +++ b/.github/workflows/push_dockerhub_rootseg_release.yml @@ -1,4 +1,4 @@ -name: Docker push for rootseg container (dev) +name: Docker push for rootseg container (release) # This builds the docker image and pushes to DockerHub on: @@ -7,7 +7,7 @@ on: jobs: push_dockerhub: - name: Push new docker image to DockerHub (dev) + name: Push new docker image to DockerHub (release) runs-on: ubuntu-latest # Only run for the nf-core repo, for releases and merged PRs if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }} @@ -19,9 +19,9 @@ jobs: uses: actions/checkout@v2 - name: Build new docker image - run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtarootseg:dev + run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtarootseg:latest - - name: Push docker image to DockerHub (dev) + - name: Push docker image to DockerHub (release) run: | echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin docker push qbicpipelines/rtarootseg:latest diff --git a/.github/workflows/push_dockerhub_rtsstat_release.yml b/.github/workflows/push_dockerhub_rtsstat_release.yml index b279a514..3bba2ab8 100644 --- a/.github/workflows/push_dockerhub_rtsstat_release.yml +++ b/.github/workflows/push_dockerhub_rtsstat_release.yml @@ -1,4 +1,4 @@ -name: Docker push for stat container (dev) +name: Docker push for stat container (release) # This builds the docker image and pushes to DockerHub on: @@ -7,7 +7,7 @@ on: jobs: push_dockerhub: - name: Push new docker image to DockerHub (dev) + name: Push new docker image to DockerHub (release) runs-on: ubuntu-latest # Only run for the nf-core repo, for releases and merged PRs if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }} @@ -19,9 +19,9 @@ jobs: uses: actions/checkout@v2 - name: Build new docker image - run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtastat:dev + run: docker build --no-cache ./modules/local/ratioconv/ -t qbicpipelines/rtastat:latest - - name: Push docker image to DockerHub (dev) + - name: Push docker image to DockerHub (release) run: | echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin docker push qbicpipelines/rtastat:latest diff --git a/README.md b/README.md index 864d715e..49c7011d 100644 --- a/README.md +++ b/README.md @@ -6,20 +6,10 @@ **A reproducible analysis pipeline for pH measurements derived from fluorescence microscopy of _A. thaliana_ root tissue**. -[![GitHub Actions CI Status](https://github.com/nf-core/rts/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rts/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/rts/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rts/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rts/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) - [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rts-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rts) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) - ## Introduction **qbic-pipelines/root-tissue-analysis** is a bioinformatics best-practice pipeline to analyze pH measurements from root tissue samples of _A. thaliana._, these measurments are derived from fluorescence microscopy images. This pipeline aims to analyze pH measurments to validate the acid-growth hypothesis, which explains the expansion of cells in root tissue. This acid-growth pathway model needs substantial pH measurement data for validation, however this type of data generation is time consuming, since manual annotation of ROIs is a mayor bottle-neck. To mitigate this issue, the pipeline provides automatic, multi-class tissue segmentation (5 clases) using U-Net models, previously trained on a dataset generated and annotated by experienced plant biologists (https://github.com/qbic-pipelines/root-tissue-segmentation-core/). @@ -70,7 +60,7 @@ Sample input data: [`Testdata`](https://github.com/qbic-pipelines/root-tissue-an #### Steps -1. Fiji macro for ratimeric image conversion ([`RATIOCONV`]) +1. Fiji macro for ratiomeric image conversion ([`RATIOCONV`]) - `RATIOCONV` container: https://hub.docker.com/r/qbicpipelines/rtaratioconv diff --git a/modules/local/omeout/main.nf b/modules/local/omeout/main.nf index 39da61e4..e2714777 100644 --- a/modules/local/omeout/main.nf +++ b/modules/local/omeout/main.nf @@ -10,7 +10,7 @@ process OMEOUT { publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - container "qbicpipelines/rtastat:dev" + container "qbicpipelines/rtastat:1.0.0" input: path(images) diff --git a/modules/local/ratioconv/main.nf b/modules/local/ratioconv/main.nf index 3bee14d1..e5a8e01c 100644 --- a/modules/local/ratioconv/main.nf +++ b/modules/local/ratioconv/main.nf @@ -10,7 +10,7 @@ process RATIOCONV { publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - container "qbicpipelines/rtaratioconv:dev" + container "qbicpipelines/rtaratioconv:1.0.0" containerOptions "--network=none --memory-swap -1 --user root" input: diff --git a/modules/local/rootseg/main.nf b/modules/local/rootseg/main.nf index 16940c8e..2a5d9d92 100644 --- a/modules/local/rootseg/main.nf +++ b/modules/local/rootseg/main.nf @@ -10,7 +10,7 @@ process ROOTSEG_PRED { publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - container "qbicpipelines/rtarootseg:dev" + container "qbicpipelines/rtarootseg:1.0.0" input: path(brightfields) diff --git a/modules/local/rtastat.nf b/modules/local/rtastat.nf index da7e251f..3460f09d 100644 --- a/modules/local/rtastat.nf +++ b/modules/local/rtastat.nf @@ -10,7 +10,7 @@ process RTASTAT { publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - container "qbicpipelines/rtastat:dev" + container "qbicpipelines/rtastat:1.0.0" input: path(metadata) diff --git a/modules/local/rtastat/main.nf b/modules/local/rtastat/main.nf index 85cc36cb..b50a3bb4 100644 --- a/modules/local/rtastat/main.nf +++ b/modules/local/rtastat/main.nf @@ -10,7 +10,7 @@ process RTASTAT { publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - container "qbicpipelines/rtastat:dev" + container "qbicpipelines/rtastat:1.0.0" input: path(metadata) diff --git a/nextflow.config b/nextflow.config index bd4c8ef9..d25562f6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -183,7 +183,7 @@ manifest { description = """""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0dev' + version = '1.0.0' doi = '' }