Merge pull request #29 from qbic-pipelines/fix/qpb-review

Fix/qpb review

.github/workflows/push_cont_ghcr_ratioconv.yml

@@ -0,0 +1,38 @@
+name: Docker push of rtaratioconv to GHCR
+# This builds the docker image and pushes it to GHCR
+# Runs on qbic-pipelines repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+jobs:
+  push_github:
+    name: Push new rtaratioconv image to GHCR
+    runs-on: ubuntu-latest
+    # Only run for the qbic-pipelines repo, for releases and merged PRs
+    if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache ./modules/local/ratioconv/ -t ghcr.io/qbic-pipelines/rtaratioconv:latest
+
+      - name: Log in to registry
+        # Update the personal access token to GITHUB_TOKEN
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin
+
+      - name: Push image to GHCR (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtaratioconv:latest ghcr.io/qbic-pipelines/rtaratioconv:dev
+          docker push ghcr.io/qbic-pipelines/rtaratioconv:dev
+
+      - name: Push image to GHCR (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtaratioconv:latest ghcr.io/qbic-pipelines/rtaratioconv:${{ github.event.release.tag_name }}
+          docker push ghcr.io/qbic-pipelines/rtaratioconv:${{ github.event.release.tag_name }}

.github/workflows/push_cont_ghcr_rootseg.yml

@@ -0,0 +1,38 @@
+name: Docker push of rtarootseg to GHCR
+# This builds the docker image and pushes it to GHCR
+# Runs on qbic-pipelines repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+jobs:
+  push_github:
+    name: Push new rtarootseg image to GHCR
+    runs-on: ubuntu-latest
+    # Only run for the qbic-pipelines repo, for releases and merged PRs
+    if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache ./modules/local/rootseg/ -t ghcr.io/qbic-pipelines/rtarootseg:latest
+
+      - name: Log in to registry
+        # Update the personal access token to GITHUB_TOKEN
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin
+
+      - name: Push image to GHCR (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtarootseg:latest ghcr.io/qbic-pipelines/rtarootseg:dev
+          docker push ghcr.io/qbic-pipelines/rtarootseg:dev
+
+      - name: Push image to GHCR (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtarootseg:latest ghcr.io/qbic-pipelines/rtarootseg:${{ github.event.release.tag_name }}
+          docker push ghcr.io/qbic-pipelines/rtarootseg:${{ github.event.release.tag_name }}

.github/workflows/push_cont_ghcr_rtsstat.yml

@@ -0,0 +1,38 @@
+name: Docker push of rtastat to GHCR
+# This builds the docker image and pushes it to GHCR
+# Runs on qbic-pipelines repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+jobs:
+  push_github:
+    name: Push new rtastat image to GHCR
+    runs-on: ubuntu-latest
+    # Only run for the qbic-pipelines repo, for releases and merged PRs
+    if: ${{ github.repository == 'qbic-pipelines/root-tissue-analysis' }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache ./modules/local/rtastat/ -t ghcr.io/qbic-pipelines/rtastat:latest
+
+      - name: Log in to registry
+        # Update the personal access token to GITHUB_TOKEN
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin
+
+      - name: Push image to GHCR (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtastat:latest ghcr.io/qbic-pipelines/rtastat:dev
+          docker push ghcr.io/qbic-pipelines/rtastat:dev
+
+      - name: Push image to GHCR (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          docker tag ghcr.io/qbic-pipelines/rtastat:latest ghcr.io/qbic-pipelines/rtastat:${{ github.event.release.tag_name }}
+          docker push ghcr.io/qbic-pipelines/rtastat:${{ github.event.release.tag_name }}

CITATIONS.md

@@ -12,7 +12,7 @@
 
 - [RootSeg](https://github.com/qbic-pipelines/rts-prediction-package)
 
-  > Heumos, L., Ehmele, P., Cuellar, L. K., Menden, K., Miller, E., Lemke, S., Gabernet, G., & Nahnsen, S. (2021). mlf-core: a framework for deterministic machine learning. In arXiv [cs.MS]. arXiv. http://arxiv.org/abs/2104.07651
+  > Heumos, L., Ehmele, P., Cuellar, L. K., Menden, K., Miller, E., Lemke, S., Gabernet, G., & Nahnsen, S. (2021). mlf-core: a framework for deterministic machine learning. Bioinformatics, 39(4). doi: [10.1093/bioinformatics/btad164](https://doi.org/10.1093/bioinformatics/btad164).
 
   - **Training module:** https://github.com/qbic-pipelines/root-tissue-segmentation-core
 

README.md

@@ -79,7 +79,7 @@ Sample input data: [`Testdata`](https://github.com/qbic-pipelines/root-tissue-an
 
 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
 
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(We strongly recommend using **Docker**, please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
 3. Download the pipeline and test with profiles:
 
@@ -137,6 +137,6 @@ An extensive list of references for the tools used by the pipeline can be found
 
 > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **The nf-core framework for community-curated bioinformatics pipelines.** Nat Biotechnol. 2020 Mar;38(3):276-278. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). PubMed PMID: 32055031.
 
-> Heumos, L., Ehmele, P., Cuellar, L. K., Menden, K., Miller, E., Lemke, S., Gabernet, G., & Nahnsen, S. (2021). **mlf-core: a framework for deterministic machine learning.** In arXiv [cs.MS]. arXiv. http://arxiv.org/abs/2104.07651
+> Heumos, L., Ehmele, P., Cuellar, L. K., Menden, K., Miller, E., Lemke, S., Gabernet, G., & Nahnsen, S. (2023). **mlf-core: a framework for deterministic machine learning.** Bioinformatics, 39(4). doi: [10.1093/bioinformatics/btad164](https://doi.org/10.1093/bioinformatics/btad164).
 
 > Barbez, E., Dünser, K., Gaidora, A., Lendl, T., & Busch, W. (2017). **Auxin steers root cell expansion via apoplastic pH regulation in Arabidopsis thaliana.** Proceedings of the National Academy of Sciences of the United States of America, 114(24), E4884–E4893.

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:1.0.0"
+    container 'ghcr.io/qbic-pipelines/rtastat:1.0.0'
 
     input:
     path(images)
@@ -35,7 +35,7 @@ process OMEOUT_UNCERT {
     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 'ghcr.io/qbic-pipelines/rtastat:1.0.0'
 
     input:
     path(images)
@@ -59,7 +59,7 @@ process OMEOUT_GGCAM {
     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 'ghcr.io/qbic-pipelines/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:1.0.0"
+    container 'ghcr.io/qbic-pipelines/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:1.0.0"
+    container 'ghcr.io/qbic-pipelines/rtarootseg:1.0.0'
 
     input:
     path(brightfields)
@@ -39,7 +39,7 @@ process ROOTSEG_UNCERT {
     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 'ghcr.io/qbic-pipelines/rtarootseg:1.0.0'
 
     input:
     path(brightfields)
@@ -68,7 +68,7 @@ process ROOTSEG_GGCAM {
     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 'ghcr.io/qbic-pipelines/rtarootseg:1.0.0'
 
     input:
     path(brightfields)

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:1.0.0"
+    container 'ghcr.io/qbic-pipelines/rtastat:1.0.0'
 
     input:
     path(metadata)