Merge branch '31-DesignFileSpace' into 'develop'

Resolve "Design file - filename with spaces error"

Closes #31 and #32

See merge request !53

CHANGELOG.md

@@ -3,6 +3,8 @@
 * Change Cellranger Version to 3.1.0
 * Fix countDesign to take multiple samples
 * Add MIT License
+* Check Design File for spaces in name
+* Update design example, README, and astrocyte.yml with current barcode IDs
 
 **Background**
 * Add CI artifacts

README.md

@@ -36,6 +36,8 @@ To Run:
     * column 1 = "Lane" (number of lanes to demultiplex, */** for all lanes)
     * column 2 = "Sample" (sample name)
     * column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
+    * Last character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in.
+    * [Current sample barcode IDs](https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv)
     * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
     * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
     * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'**
@@ -50,7 +52,7 @@ To Run:
 
 | Lane | Sample      | Index     |
 |------|-------------|-----------|
-| *    | test_sample | SI-P03-C9 |
+| *    | test_sample | SI-GA-C9 |
 
 
 [**CHANGELOG**](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/CHANGELOG.md)

astrocyte_pkg.yml

@@ -93,7 +93,7 @@ workflow_parameters:
     required: true
     regex: ".*\\.csv"
     description: |
-      A design file listing lane, sample, corresponding index.
+      A design file listing lane, sample, corresponding index (last characters represent well position of 96-well plate). [Current sample barcode IDs](https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv)
 
 
 # -----------------------------------------------------------------------------

docs/design.csv

 Lane,Sample,Index
-1,test_sample,SI-P03-C9
+1,test_sample,SI-GA-C9

docs/index.md

@@ -31,7 +31,7 @@ To Run:
 
     | Lane | Sample      | Index     |
     |------|-------------|-----------|
-    | *    | test_sample | SI-P03-C9 |
+    | *    | test_sample | SI-GA-C9 |
     
 
 

workflow/main.nf

@@ -50,7 +50,11 @@ process checkDesignFile {
     """
     hostname
     ulimit -a
-    python3 ${baseDir}/scripts/check_design.py -d ${designLocation}
+    noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
+    if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
+      mv "${designLocation}" "\${noSpaceDesign}"
+    fi
+    python3 ${baseDir}/scripts/check_design.py -d \${noSpaceDesign}
     """
 
 }
@@ -201,4 +205,4 @@ process multiqc {
     multiqc -c ${multiqcConf} .
     """
 
-}
\ No newline at end of file
+}