Allow for custom -X while using 10xFB workflow #299
Description
Describe the issue
Allow for a custom -x parameter when using the 10xFB workflow.
This is important when features (like crispr guides) are expected to be found in an exact region of the read. For example, 0,0,16:0,16,28:1,30,51 .The current default will force the 10xv3, but would try to map the feature in the whole read2.
What is the exact command that was run?
kb count -i guide_index.idx -g t2guide.txt --verbose -w barcode_file.txt --h5ad --kallisto /opt/conda/envs/nfenv/bin/kallisto --bustools /opt/conda/envs/nfenv/bin/bustools --workflow 10xFB -x 0,0,16:0,16,28:1,30,51 -o 1_ks_guide_out -t 8 SRR19330404_1.fastq SRR19330404_2.fastq SRR19330632_1.fastq SRR19330632_2.fastq SRR19330643_1.fastq SRR19330643_2.fastq SRR19330707_1.fastq SRR19330707_2.fastq --overwrite