Add process for building cellranger index to build-index.nf

[allyhawkins]

Closes #65. This PR adds the cellranger_index process to the workflow for building the indices, build-index.nf ensuring that when we build all of our indices they will use the same assembly. I followed the same setup that was previously used in generating the cellranger index in alsf-scpca/workflows/rnaseq-ref-index/build-cellranger-index.nf.

This was pretty straight forward and I was able to test it and everything ran successfully, producing a new index with ensembl 104. The only question I had was about how we wanted to name this index. I included the assembly name that we use in the splici index and then appended _cdna_cellranger, but let me know if there is a different naming convention that would be preferred.

[jashapiro]

This looks good. I made a couple of suggestions below, which might make this index more comparable to the one we use for salmon.

I was going to make an additional suggestion about naming params, but ended up putting it in a separate issue: #67

[jashapiro]

Is this going to be too stringent? I would think we should include ncRNA and such: The default cellranger index includes much more: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#mkgtf

(I just looked at the full list of gene_biotypes in the reference we are using, which appears below (generated with grep -o 'gene_biotype [^;]*' Homo_sapiens.GRCh38.104.gtf |sort | uniq) and noted that the code used by 10X might miss lncRNA as it is looking for lincRNA, according to that page.)

Alternatively, we could probably just not filter the gtf file? This would probably be more comparable to what we have for the salmon index, which I do not think we filter at all (hence 60K "genes").

gene_biotype "IG_C_gene"
gene_biotype "IG_C_pseudogene"
gene_biotype "IG_D_gene"
gene_biotype "IG_J_gene"
gene_biotype "IG_J_pseudogene"
gene_biotype "IG_V_gene"
gene_biotype "IG_V_pseudogene"
gene_biotype "IG_pseudogene"
gene_biotype "Mt_rRNA"
gene_biotype "Mt_tRNA"
gene_biotype "TEC"
gene_biotype "TR_C_gene"
gene_biotype "TR_D_gene"
gene_biotype "TR_J_gene"
gene_biotype "TR_J_pseudogene"
gene_biotype "TR_V_gene"
gene_biotype "TR_V_pseudogene"
gene_biotype "lncRNA"
gene_biotype "miRNA"
gene_biotype "misc_RNA"
gene_biotype "polymorphic_pseudogene"
gene_biotype "processed_pseudogene"
gene_biotype "protein_coding"
gene_biotype "pseudogene"
gene_biotype "rRNA"
gene_biotype "rRNA_pseudogene"
gene_biotype "ribozyme"
gene_biotype "sRNA"
gene_biotype "scRNA"
gene_biotype "scaRNA"
gene_biotype "snRNA"
gene_biotype "snoRNA"
gene_biotype "transcribed_processed_pseudogene"
gene_biotype "transcribed_unitary_pseudogene"
gene_biotype "transcribed_unprocessed_pseudogene"
gene_biotype "translated_processed_pseudogene"
gene_biotype "translated_unprocessed_pseudogene"
gene_biotype "unitary_pseudogene"
gene_biotype "unprocessed_pseudogene"
gene_biotype "vault_RNA"

[allyhawkins]

We definitely don't do any filtering like this for the salmon index, so I can remove this to make it more comparable.

[allyhawkins]

I went ahead and removed filtering and it worked fine, creating a larger index this time.

[jashapiro]

Looks good, with two small suggestions I made, and one that I can't actually put in, which is to add

  cellranger_index = "s3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-104/cellranger_index/Homo_sapiens.GRCh38.104_cellranger_full"

to the params in nextflow.config

[jashapiro]

I think you can actually completely skip mkgtf as I don't think it is doing anything here.

Suggested change

	cellranger mkgtf \
	genome.gtf \
	filtered.gtf
	cellranger mkref \
	--genome=${cellranger_index} \
	--fasta=genome.fasta \
	--genes=filtered.gtf \
	cellranger mkref \
	--genome=${cellranger_index} \
	--fasta=genome.fasta \
	--genes=genome.gtf \

[allyhawkins]

@jashapiro I went ahead and made the edits that you suggested and then also had to increase the memory that the process is using. I noticed that it was only making some of the index files but not all of them even though it was completing the process successfully without error. It wasn't until I attempted to run spaceranger using the index later on that I realized there was missing files and only a partial index so had to bump up the memory required too.

[jashapiro]

LGTM!