Add Seurat version to report and fix Seurat itteration

docs/references.md

 ### References
 
 1. **Nextflow**:
-  * Di Tommaso P., Chatzou M., Floden E. W., Barja P. P., Palumbo E., and Notredame C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology 35(4): 316. doi:[10.1038/nbt.3820](https://doi.org/10.1038/nbt.3820)
+  * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319. doi:[10.1038/nbt.3820](https://doi.org/10.1038/nbt.3820)
 
 2. **cellranger**
   * Cellranger count [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count)
@@ -9,5 +9,8 @@
 3. **python**:
   * Anaconda (Anaconda Software Distribution, [https://anaconda.com](https://anaconda.com))
 
-4. **MultiQc**:
+4. **Seurat**:
+  * Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck III, W. M., ... & Satija, R. (2019). Comprehensive integration of single-cell data. Cell, 177(7), 1888-1902. doi:[10.1016/j.cell.2019.05.031](https://doi.org/10.1016/j.cell.2019.05.031)
+
+5. **MultiQc**:
   * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)

workflow/configs/cluster.config

@@ -24,13 +24,13 @@ process {
   withName: count400 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
+  withName: downstreamViz {
+    queue = '32GB'
+  }
   withName: versions {
     executor = 'local'
   }
   withName: multiqc {
     executor = 'local'
   }
-  withName: downstreamViz {
-    executor = '32GB'
-  }
 }

workflow/main.nf

@@ -88,6 +88,7 @@ filename_checkScript = Channel.fromPath("$baseDir/scripts/filename_check.sh")
 generate_versionsScript = Channel.fromPath("$baseDir/scripts/generate_versions.py")
 generate_referencesScript = Channel.fromPath("$baseDir/scripts/generate_references.py")
 versions_pythonScript = Channel.fromPath("$baseDir/scripts/versions_python.sh")
+versions_seuratScript = Channel.fromPath("$baseDir/scripts/versions_seurat.sh")
 downstream_vizScript = Channel.fromPath("$baseDir/scripts/downstream_viz.r")
 
 // Define report files
@@ -373,6 +374,37 @@ process count400 {
     }
 }
 
+// Collect all outputs reguardless of cellranger version
+filteredOut = filteredOut211.mix(filteredOut302, filteredOut310, filteredOut400)
+// Combine all inputs for downstreamViz
+downstreamVizIn = downstream_vizScript.combine(versions_seuratScript).combine(filteredOut)
+
+/*
+ * downstreamViz: create files for downstream use (eg. R Seurat object)
+ */
+process downstreamViz {
+  tag "${sample}"
+  publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "*.rds"
+  module 'seurat/3.0.0'
+
+  input:
+    set file("*"), file("*"), sample, file("filtered/*"), file("clustering/graphclust/*"), file("clustering/kmeans_2_clusters/*"), file("clustering/kmeans_3_clusters/*"), file("clustering/kmeans_4_clusters/*"), file("clustering/kmeans_5_clusters/*"), file("clustering/kmeans_6_clusters/*"), file("clustering/kmeans_7_clusters/*"), file("clustering/kmeans_8_clusters/*"), file("clustering/kmeans_9_clusters/*"), file("clustering/kmeans_10_clusters/*"), file("pca/*"), file("tsne/*"), file("umap/*") from downstreamVizIn
+    //file downstream_vizScript
+    //file versions_seuratScript
+
+  output:
+    file "*.rds" into seuratPaths
+    file "version_seurat.txt" into version_seurat
+
+  script:
+    """
+    hostname
+    ulimit -a
+    seurat-Rscript downstream_viz.r --sample ${sample} --cellrangerVersion ${version}
+    bash versions_seurat.sh > version_seurat.txt
+    """
+}
+
 /*
  * versions: collect all versions into a single yml
  */
@@ -382,6 +414,7 @@ process versions {
 
   input:
     file versions_pythonScript
+    file version_seurat
     file generate_versionsScript
     file generate_referencesScript
 
@@ -428,29 +461,3 @@ process multiqc {
     multiqc -c ${multiqcConf} .
     """
 }
-
-// Collect all outputs reguardless of cellranger version
-filteredOut = filteredOut211.mix(filteredOut302, filteredOut310, filteredOut400)
-
-/*
- * downstreamViz: create files for downstream use (eg. R Seurat object)
- */
-process downstreamViz {
-  tag "${sample}"
-  publishDir "${outDir}/${task.process}", mode: 'copy'
-  module 'seurat/3.0.0'
-
-  input:
-    file downstream_vizScript
-    set sample, file("filtered/*"), file("clustering/graphclust/*"), file("clustering/kmeans_2_clusters/*"), file("clustering/kmeans_3_clusters/*"), file("clustering/kmeans_4_clusters/*"), file("clustering/kmeans_5_clusters/*"), file("clustering/kmeans_6_clusters/*"), file("clustering/kmeans_7_clusters/*"), file("clustering/kmeans_8_clusters/*"), file("clustering/kmeans_9_clusters/*"), file("clustering/kmeans_10_clusters/*"), file("pca/*"), file("tsne/*"), file("umap/*") from filteredOut
-
-  output:
-    file "*.rds" into seuratPaths
-
-  script:
-    """
-    hostname
-    ulimit -a
-    seurat-Rscript downstream_viz.r --sample ${sample} --cellrangerVersion ${version}
-    """
-}

workflow/scripts/generate_versions.py

@@ -28,6 +28,7 @@ SOFTWARE_REGEX = {
     'Nextflow': ['version_nextflow.txt', r"(\S+)"],
     'cellranger count': ['version_cellranger.txt', r"(\S+)"],
     'python': ['version_python.txt', r"(\S+)"],
+    'seurat': ['version_seurat.txt', r"(\S+)"],
 }
 
 
@@ -77,6 +78,7 @@ def main():
     results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
     results['cellranger count'] = '<span style="color:#999999;\">N/A</span>'
     results['python'] = '<span style="color:#999999;\">N/A</span>'
+    results['seurat'] = '<span style="color:#999999;\">N/A</span>'
 
     # Check for version files:
     check_files(files)

workflow/scripts/versions_seurat.sh

+#!/bin/bash
+#versions_python.sh
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
+seurat-Rscript -e 'packageVersion("Seurat")' |& grep '\[1\] ' | sed -n -e 's/^\[1\] ‘//p' | tr -d '’'