Merge pull request #53 from CaroAMN/dev

Adding review suggestions

Author: CaroAMN

.gitignore

@@ -8,4 +8,3 @@ testing*
 *.pyc
 null/
 .nf-test*
-.nf-test/

CITATIONS.md

@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [NuMorph](https://pubmed.ncbi.nlm.nih.gov/34644582/)
-
-> Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL. NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images. Cell Rep. 2021 Oct 12;37(2):109802. doi: 10.1016/j.celrep.2021.109802. PMID: 34644582; PMCID: PMC8530274.
-
 - [BaSiC](https://www.nature.com/articles/ncomms14836)
 
 > Peng, T., Thorn, K., Schroeder, T. et al. A BaSiC tool for background and shading correction of optical microscopy images. Nat Commun 8, 14836 (2017). https://doi.org/10.1038/ncomms14836
@@ -22,17 +18,21 @@
 
 > Klein S, Staring M, Murphy K, Viergever MA, Pluim JP. elastix: a toolbox for intensity-based medical image registration. IEEE Trans Med Imaging. 2010 Jan;29(1):196-205. doi: 10.1109/TMI.2009.2035616. Epub 2009 Nov 17. PMID: 19923044.
 
-- [3DUnetCNN](https://pubmed.ncbi.nlm.nih.gov/37555134/)
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-> Ellis DG, Aizenberg MR. Structural Brain Imaging Predicts Individual-Level Task Activation Maps Using Deep Learning. Front Neuroimaging. 2022 Apr 18;1:834883. doi: 10.3389/fnimg.2022.834883. PMID: 37555134; PMCID: PMC10406267.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+
+- [NuMorph](https://pubmed.ncbi.nlm.nih.gov/34644582/)
+
+> Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL. NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images. Cell Rep. 2021 Oct 12;37(2):109802. doi: 10.1016/j.celrep.2021.109802. PMID: 34644582; PMCID: PMC8530274.
 
 [VLFeat](https://www.vlfeat.org/)
 
 > A. Vedaldi and B. Fulkerson VLFeat: An Open and Portable Library of Computer Vision Algorithms (2008)
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [3DUnetCNN](https://pubmed.ncbi.nlm.nih.gov/37555134/)
 
-> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ellis DG, Aizenberg MR. Structural Brain Imaging Predicts Individual-Level Task Activation Maps Using Deep Learning. Front Neuroimaging. 2022 Apr 18;1:834883. doi: 10.3389/fnimg.2022.834883. PMID: 37555134; PMCID: PMC10406267.
 
 ## Software packaging/containerisation tools
 

README.md

@@ -24,9 +24,7 @@
 
 **nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleared samples. The pipeline takes raw images from a directory or a zip archive as input. The images need to be in a 2D single-channel 16-bit `tif`format.
 
-<div style="text-align: center;">
-<img src="docs/images/lsmquant-metromap.svg" alt="lasmquant metromap">
-</div>
+![lsmquant metromap](docs/images/lsmquant-metromap.svg)
 
 ## Pipeline Summary
 
@@ -42,14 +40,14 @@ This stage reconstructs the 3D image from raw light-sheet data. Here three diffe
 
 3. `stitch_only`: Performs only iterative tile stitching
 
-**Allen Brain Atlas Registration (Optional)**
-
-This workflow registers full brain images to the Allen Brain Reference Atlas. This is an optional workflow and can be chosen by setting the parameter: `ara_registartion`
-
 **Cell Nuclei Quantification**
 
 Quantification of cell-nuclei is performed using a 3D-Unet and it is performed on the nuclear channel only. This is an optional workflow and can be chosen by setting the parameter:`nuclei_quantification`
 
+**Allen Brain Atlas Registration (Optional)**
+
+This workflow registers full brain images to the Allen Brain Reference Atlas. This is an optional workflow and can be chosen by setting the parameter: `ara_registartion`
+
 ## Usage
 
 > [!NOTE]
@@ -67,7 +65,6 @@ TEST1,path/to/image-files,path/to/parameter/file.csv
 The parameter csv file includes sample specific parameters that are used for processing the given data. It needs to follow a specific structure.
 
 Please get the basic template file [here](../assets/params_template_lsmquant.csv).
-`parametersheet.csv`
 
 Now, you can run the pipeline using:
 

conf/base.config

@@ -51,11 +51,6 @@ process {
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:process_high_long {
-        cpus   = { 6     * task.attempt }
-        memory = { 36.GB * task.attempt }
-        time   = { 24.h   * task.attempt }
-    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }
@@ -67,19 +62,5 @@ process {
         ext.use_gpu = true
         accelerator = 1
     }
-    withName: 'NUMORPHINTENSITY' {
-        cpus   = { 2     * task.attempt }
-        memory = { 30.GB * task.attempt }
-        time   = { 2.h  * task.attempt }
-    }
-    withName: 'NUMORPHALIGN' {
-        cpus   = { 7     * task.attempt }
-        memory = { 6.GB * task.attempt }
-        time   = { 11.h  * task.attempt }
-    }
-    withName: 'NUMORPHSTITCH' {
-        cpus   = { 2     * task.attempt }
-        memory = { 9.GB * task.attempt }
-        time   = { 15.h  * task.attempt }
-    }
+
 }

conf/modules.config

@@ -34,6 +34,9 @@ process {
     }
 
     withName: 'NUMORPHINTENSITY' {
+        cpus   = { 2     * task.attempt }
+        memory = { 30.GB * task.attempt }
+        time   = { 2.h  * task.attempt  }
         publishDir = [
             path: { "${params.outdir}/numorphintensity/" },
             mode: params.publish_dir_mode,
@@ -49,6 +52,9 @@ process {
     }
 
     withName: 'NUMORPHALIGN' {
+        cpus   = { 7     * task.attempt }
+        memory = { 6.GB * task.attempt  }
+        time   = { 11.h  * task.attempt }
         publishDir = [
             path: { "${params.outdir}/numorphalign/" },
             mode: params.publish_dir_mode,
@@ -64,10 +70,13 @@ process {
     }
 
     withName: 'NUMORPHSTITCH' {
+        cpus   = { 2     * task.attempt }
+        memory = { 9.GB * task.attempt  }
+        time   = { 15.h  * task.attempt }
         publishDir = [
             path: { "${params.outdir}/numorphstitch/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/**/*',
+            pattern: 'results/*',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
@@ -110,15 +119,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/numorph3dunet/" },
             mode: params.publish_dir_mode,
-            pattern: 'results/*',
-            saveAs: { filename ->
-                if (filename.equals('versions.yml')) {
-                    null
-                }
-                else {
-                    filename.replaceFirst("^results/", "${meta.id}/")
-                }
-            }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }