Merge pull request #61 from nf-core/dev

Patch release 1.0.1

Author: CaroAMN

.nf-core.yml

@@ -1,11 +1,10 @@
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 lint:
-  included_configs: False
+  included_configs: false
 template:
   author: Carolin Schwitalla
-  description: A pipeline for preprocessing and analysis of large-scale light-sheet
-    microscopy images based on the NuMorph toolbox
+  description: A pipeline for preprocessing and analysis of large-scale light-sheet microscopy images based on the NuMorph toolbox
   force: false
   is_nfcore: true
   name: lsmquant
@@ -14,4 +13,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 1.0.0
+  version: 1.0.1

CHANGELOG.md

@@ -3,6 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.0.1 - Excited Squid Patch
+
+### `Fixed`
+
+- [PR#57](https://github.com/nf-core/lsmquant/pull/57) - Fix input declaration of the model file for the module: `numorph3dunet` to be reused for all inputs.
+- remove conda batch from readme, the pipeline does not support conda.
+- set matlab cache directory in numorph_stitch to fix concurrency issues when running multiple samples.
+
 ## v1.0.0 - Excited Squid
 
 Initial release of nf-core/lsmquant, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -12,7 +12,6 @@
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
-[![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/)
 [![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)

assets/multiqc_config.yml

@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/lsmquant/releases/tag/1.0.0" target="_blank">nf-core/lsmquant</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/lsmquant/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/lsmquant/releases/tag/1.0.1" target="_blank">nf-core/lsmquant</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/lsmquant/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-lsmquant-methods-description":
     order: -1000

modules/local/numorphstitch/main.nf

@@ -23,6 +23,8 @@ process NUMORPHSTITCH {
     def NM_var = NM_variable ? NM_variable : ''
     def variables_input = variables ? variables : ''
     """
+    export MCR_CACHE_ROOT=\${PWD}/.mcrCache
+
     # create output directories needed by the tool
     mkdir -p ./results/stitched/
 

nextflow.config

@@ -250,7 +250,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.0.0'
+    version         = '1.0.1'
     doi             = ''
 }
 

ro-crate-metadata.json

@@ -25,7 +25,7 @@
                     "numorph_param_validation": "1.0.0"
                 },
                 "Workflow": {
-                    "nf-core/lsmquant": "v1.0.0"
+                    "nf-core/lsmquant": "v1.0.1"
                 }
             },
             [
@@ -79,7 +79,7 @@
                 "params_TEST1_lsmquant.csv:md5,a1edc3a22e8f390e473102d0193a8f1c"
             ]
         ],
-        "timestamp": "2026-03-20T13:18:41.89714723",
+        "timestamp": "2026-04-29T15:18:49.500188714",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.3"
@@ -111,7 +111,7 @@
                     "numorph_param_validation": "1.0.0"
                 },
                 "Workflow": {
-                    "nf-core/lsmquant": "v1.0.0"
+                    "nf-core/lsmquant": "v1.0.1"
                 }
             },
             [
@@ -579,7 +579,7 @@
                 "params_TEST1_lsmquant.csv:md5,a1edc3a22e8f390e473102d0193a8f1c"
             ]
         ],
-        "timestamp": "2026-03-20T13:17:57.078651506",
+        "timestamp": "2026-04-29T15:16:32.417361365",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.3"

tests/default.nf.test.snap

@@ -134,14 +134,14 @@ workflow LSMQUANT {
 
     stitched_data = ch_samplesheet
             .join (stitched_output)
-            .map { meta, img_dir, parameter_file, stitched_data ->
+            .map { meta, img_directory, parameter_file, stitched_data ->
                 [meta, stitched_data, parameter_file]
             }
 
     // run nuclei quantification
     if (params.nuclei_quantification) {
 
-        def model_file = Channel.fromPath(params.model_file, checkIfExists: !params.model_file.startsWith('http'))
+        model_file = file(params.model_file, checkIfExists: !params.model_file.startsWith('http'))
         NUMORPH3DUNET (stitched_data, model_file)
 
     }