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BICF
Astrocyte
cellranger_mkfastq
Commits
d770f29d
Commit
d770f29d
authored
Jun 21, 2020
by
Gervaise Henry
🤠
Browse files
Version 2.1.4
parent
9c4cf485
Pipeline
#7375
passed with stages
in 6 minutes and 38 seconds
Changes
4
Pipelines
1
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CHANGELOG.md
View file @
d770f29d
# v2.1.
2
# v2.1.
4
**UserFacing**
*
Check Design File for spaces in name and file contents
*
Update design example, README, and astrocyte.yml with current barcode IDs
...
...
README.md
View file @
d770f29d
...
...
@@ -48,19 +48,22 @@ To Run:
*
run name, puts outputs in a directory with this name
*
eg:
**--name 'test'**
*
**--bcl**
*
B
ase call files (tarballed [
*.tar] +/- gunzipping [*
.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
.
*
T
here can be multiple basecall files, but they all will be demultiplexed by the same design file
.
*
b
ase call files (tarballed [
*.tar] +/- gunzipping [*
.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
*
t
here can be multiple basecall files, but they all will be demultiplexed by the same design file
*
eg:
```--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'```
*
**--designFile**
*
path to design file (csv format) location
*
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)
*
L
ast character set in Index references the well position of the 96-well plate that the sample barcode kit is sold in
.
*
l
ast 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'```
*
**--mask**
*
add a base mask if the sequencing strategy doesn't match the requirements of 10x Genomics
*
eg:
**--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'**
*
**--outDir**
*
optional output directory for run
*
eg:
```--outDir 'test'```
...
...
@@ -70,8 +73,8 @@ To Run:
```
*
Design example:
| Lane | Sample | Index
|
|------|-------------|----------
-
|
| Lane | Sample | Index |
|------|-------------|----------|
|
*
| test_sample | SI-GA-C9 |
...
...
workflow/main.nf
View file @
d770f29d
...
...
@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.
3
"
pipelineVersion = "2.1.
4
"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
...
...
workflow/nextflow.config
View file @
d770f29d
...
...
@@ -47,6 +47,6 @@ manifest {
homePage
=
'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description
=
'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript
=
'main.nf'
version
=
'2.1.
2
'
version
=
'2.1.
4
'
nextflowVersion
=
'>=0.31.0'
}
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