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Commit 696f2ff1 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch '31-DesignFileSpace' into 'develop'

Resolve "Design file - filename with spaces error"

Closes #31 and #32

See merge request !53
parents d9eb45c1 c3627214
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3 merge requests!59Develop,!58Develop,!53Resolve "Design file - filename with spaces error"
Pipeline #4846 passed with stages
in 2 minutes and 27 seconds
......@@ -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
......
......@@ -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)
......
......@@ -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)
# -----------------------------------------------------------------------------
......
Lane,Sample,Index
1,test_sample,SI-P03-C9
1,test_sample,SI-GA-C9
......@@ -31,7 +31,7 @@ To Run:
| Lane | Sample | Index |
|------|-------------|-----------|
| * | test_sample | SI-P03-C9 |
| * | test_sample | SI-GA-C9 |
......
......@@ -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
}
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