* Adjust versions to take into account multiple 10x-Ranger softwares
* Remove countDesign process
* Spaceranger V1.2.0 update
**Background**
*
* Update scripts to reflect spaceranger or cellranger input
* Update CI to include simple3 and add simple3 tests for later pytest use (commented out for all simple CI)
* Add simple3 to test data folder
* redo channels to include multple rangers
* Rename simple1 and 2 to cellranger1 and 2 and simple3 to spaceranger1
* Redo Versioning for rangers to ouput correctly
*Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
This pipeline is a wrapper for the cellranger or spaceranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
...
...
@@ -42,15 +42,19 @@ To Run:
* Available parameters:
***-profile**
* what environments to run on, available: `biohpc`, `local`, `cluster`, `aws`, `ondemand`, `spot`
* eg: **-profile biohpc,cluster** to run on BioHPC in cluster mode
* eg: **-profile aws,ondemand** to run on AWS on a on-demand queue
* eg: `-profile biohpc,cluster` to run on BioHPC in cluster mode
* eg: `-profile aws,ondemand` to run on AWS on a on-demand queue
***--name**
* run name, puts outputs in a directory with this name
* eg: **--name 'test'**
* eg: `--name 'test'`
***--ranger**
* select the 10x ranger being run.
* eg: `--ranger 'cellranger'` to run cellranger mkfastq
* eg: `--ranger 'spaceranger'` to run spaceranger mkfastq
***--bcl**
* base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
* there can be multiple basecall files, but they all will be demultiplexed by the same design file
This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
This pipeline is a wrapper for the various ranger mkfastq tools from 10x Genomics (which uses Illumina's bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
* 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)
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* 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)