* Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs
* Remove unnecessary intermediate process files
* Add config option for running on AWS
* Ignore dual index
* Add parameter for base mask (not available in Astrocyte)
* Output Nextflow version in QC report
* Output pipeline version (manual) in QC report
**Background**
* Add Nextflow Tower integration into CI (GHH's profile)
* Utilize BICF docker containers
* Update to be runnable on cloud
* Refactor configs
*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 also capable of being run on AWS. To do so:
* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
*Edit one of the aws configs in workflow/config/
*In the aws configs in `workflow/configs/`:
* Replace workDir with the S3 bucket generated
* Change region if different
* Change queue to the aws batch queue generated
* In the ondemand and spot configs in `workflow/config/`:
* Change queue to the aws batch queues generated
* The user must be have awscli configured with an appropriate authentication (with ```aws configure``` and access keys) in the environment which nextflow will be run
* Add ```-profile ``` with the name aws config which was custamized
* eg. ```nextflow run workflow/main.nf -profile aws_ondemand```
* Add ```-profile ``` with aws and the queue config which was customized
* eg. ```nextflow run workflow/main.nf -profile aws,ondemand```
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
***--name**
* run name, puts outputs in a directory with this name
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)
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 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.
FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.