Merge pull request #28 from qbic-pipelines/dev

Fixed versioning

.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

.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

.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

.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

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
 

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)

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:

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)

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)

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)

nextflow.config

@@ -183,7 +183,7 @@ manifest {
     description     = """"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.0dev'
+    version = '1.0.0'
     doi             = ''
 }