update pipeline level test

.github/workflows/nf-test-gpu.yml

@@ -71,7 +71,7 @@ jobs:
       needs.get-shards.outputs.total_shards > 0 &&
       (
         github.event_name != 'push' ||
-        ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' )
+        ( github.event_name == 'push' && github.repository == 'nf-core/lsmquant' )
       )
     strategy:
       fail-fast: false
@@ -88,6 +88,13 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Test CUDA
+        run: |
+          nvidia-smi -L
+
+      - name: Enable Nextflow debug logging
+        run: echo "NXF_DEBUG=2" >> $GITHUB_ENV
+
       - name: Run nf-test Action
         uses: ./.github/actions/nf-test
         with:
@@ -97,6 +104,10 @@ jobs:
           filters: ${{ matrix.filters }}
           tags: "gpu"
 
+      - name: Show Singularity run commands
+        run: |
+          find . -name ".nextflow.log" -exec grep "singularity exec" {} + || echo "No singularity exec found"
+
   confirm-pass:
     runs-on:
       - runs-on=${{ github.run_id }}-confirm-pass

README.md

@@ -17,13 +17,14 @@
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/lsmquant)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23lsmquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/lsmquant)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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)
+![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)
 
 ## Introduction
 
 **nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleard samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignemnt, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a regsitration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.
 
 <div style="text-align: center;">
-<img src="docs/images/lsmquant.png" alt="lasmquant metromap">
+<img src="docs/images/lsmquant-metromap.svg" alt="lasmquant metromap">
 </div>
 
 ### Basic workflow

conf/modules.config

@@ -30,174 +30,102 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
+    /*
     withName: 'MAT2JSON' {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/mat2json" },
             mode: params.publish_dir_mode
         ]
     }
+    */
+
     withName: 'NUMORPHINTENSITY' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/intensity/samples" },
-            mode: params.publish_dir_mode,
-            pattern: 'results/samples/intensity_adjustment/*',
-            saveAs: { filename ->
-                if (filename.equals('versions.yml')) {
-                    null
-                } else {
-                    filename.replaceFirst('^results/samples/intensity_adjustment/', 'samples/intensity_adjustment/')
-                }
-            }
-        ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/intensity/variables" },
+            path: { "${params.outdir}/numorphintensity/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/variables/*',
+            pattern: 'results/**/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 } else {
-                    filename.replaceFirst('^results/variables/', 'variables/')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/intensity/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-
-        ]
-
     }
 
     withName: 'NUMORPHALIGN' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/alignment/samples" },
+            path: { "${params.outdir}/numorphalign/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/samples/alignment/*',
+            pattern: 'results/**/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 } else {
-                    filename.replaceFirst('^results/samples/alignment/', 'samples/alignment/')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/alignment/variables" },
-            mode: params.publish_dir_mode,
-            pattern: 'results/variables/*',
-            saveAs: { filename ->
-                if (filename.equals('versions.yml')) {
-                    null
-                } else {
-                    filename.replaceFirst('^results/variables/', 'variables/')
-                }
-            }
-        ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/alignment/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
     withName: 'NUMORPHSTITCH' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/stitching/variables" },
+            path: { "${params.outdir}/numorphstitch/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/variables/*',
+            pattern: 'results/**/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 } else {
-                    filename.replaceFirst('^results/variables/', 'variables/')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/stitching/stitched" },
-            mode: params.publish_dir_mode,
-            pattern: 'results/stitched/*',
-            saveAs: { filename ->
-                if (filename.equals('versions.yml')) {
-                    null
-                } else {
-                    filename.replaceFirst('^results/stitched/', 'stitched/')
-                }
-            }
-        ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/stitching/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
     withName: 'NUMORPHRESAMPLE' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/resampling/resampled/" },
+            path: { "${params.outdir}/numorphresample/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/resampled/*',
+            pattern: 'results/**/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 } else {
-                    filename.replaceFirst('^results/resampled/', 'resampled/')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/resampling/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
     withName: 'NUMORPHREGISTER' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/register/registered/" },
+            path: { "${params.outdir}/numorphregister/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/registered/*',
+            pattern: 'results/**/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 } else {
-                    filename.replaceFirst('^results/registered/', 'registered/')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/register/variables" },
-            mode: params.publish_dir_mode,
-            pattern: 'results/variables/*',
-            saveAs: { filename ->
-                if (filename.equals('versions.yml')) {
-                    null
-                } else {
-                    filename.replaceFirst('^results/variables/', 'variables/')
-                }
-            }
-        ]
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/register/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
     withName: 'NUMORPH3DUNET' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/segmentation/" },
+            path: { "${params.outdir}/numorph3dunet/" },
             mode: params.publish_dir_mode,
             pattern: 'results/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
                 }
                 else {
-                    filename.replaceFirst('^results/', '')
+                    filename.replaceFirst("^results/", "${meta.id}/")
                 }
             }
         ]
     }
+
 }

conf/test.config

@@ -16,11 +16,18 @@ process {
         memory: '15.GB',
         time: '1.h'
     ]
+
+    withLabel: process_gpu {
+        ext.use_gpu = true
+        accelerator = 1
+        //containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' }
+        memory = { 15.GB * task.attempt }
+    }
 }
 
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
     input  = params.pipelines_testdata_base_path + '/test_data/samplesheets/sample_sheet.csv'
-    stage  = 'preprocessing'
+    stage  = 'full'
 }

modules.json

@@ -7,7 +7,7 @@
                 "nf-core": {
                     "basicpy": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
@@ -17,12 +17,12 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8",
                         "installed_by": ["modules"]
                     },
                     "unzip": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "unzipfiles": {
@@ -36,17 +36,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/mat2json/main.nf

@@ -23,7 +23,7 @@ process MAT2JSON {
     """
     mkdir -p ${process}
     for matfile in ${matfiles.join(' ')}; do
-        /usr/bin/mlrtapp/mat2json \$matfile
+        mat2json \$matfile
     done
 
     mv -f *.json ${process}/ 2>/dev/null || true