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github.com/denis-yuen/test-notebooks/ibm-mlb
No full textThis repo contains sample notebook files adapted from:
The Jupyter project
[github](https://github.com/jupyter/notebook/tree/main/docs/source/examples/Notebook)
[license](https://github.com/jupyter/notebook/blob/main/LICENSE)
IBM:
[github](https://github.com/ibm-et/jupyter-samples)
[license](https://github.com/ibm-et/jupyter-samples/blob/master/LICENSE
dockstore.org/denis-yuen/testwdl
No full textnot. A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information
dockstore.org/denis-yuen/testwdl
No full textnot. A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information
github.com/denis-yuen/bcellmagic
No full textB cell repertoire analysis pipeline with immcantation framework.
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/bcellmagic --reads '*_R{1,2}.fastq.gz' -profile standard,docker
Mandatory arguments:
--cprimers Path to CPrimers FASTA File
--vprimers Path to VPrimers FASTA File
--metadata Path to Metadata TSV
--umi_length Length of UMI barcodes
-profile Configuration profile to use. Can use multiple (comma separated)
Available: standard, conda, docker, singularity, awsbatch, test
Options:
References: If not specified in the configuration file or you wish to overwrite any of the references.
--imgtdb_base Path to predownloaded imgtDB
--igblast_base Path to predownloaded igblastDB
Define clones:
--set_cluster_threshold Set this parameter to allow manual hamming distance threshold for cell cluster definition.
--cluster_threshold Once set_cluster_threshold is true, set cluster_threshold value (float).
Index file:
--index_file If the unique molecular identifiers (UMI) are available in a separate index file, merge it to R1 reads.
--umi_position If UMI are not available in a separate index file, but already merged with the R1, and R2 reads, speciffy position (R1/R2).
Repertoire downstream analysis:
--downstream_only If tables are provided in option `--changeo_tables`, then perform only cluster and repertoire analysis steps.
--changeo_tables Provide Changeo table in '.tsv' if only downstream analysis is desired.
--skipDownstream Skip downstream clonal and repertoire analysis steps.
Other options:
--outdir The output directory where the results will be saved
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
--maxMultiqcEmailFileSize Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
AWSBatch options:
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion The AWS Region for your AWS Batch job to run o
github.com/denis-yuen/hello-dockstore-workflow/hello-world
No full textReverse the lines in a document, then sort those lines
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