R version to use

[mcortes-lopez]

Hi, I was wondering if is possible to use a custom conda environment?

I tried running the following command:

nextflow run GoekeLab/bambu-SingleCell-Spatial --bams ${bam} \
    --genome ${genome} \
    --annotation ${annotation} \
    --ncore 8 --outdir output \
    -with-singularity lingminhao/bambusc

Adding also -r main after loading my conda environment at some point but it returned an error related to not finding devtools installed.

Also, I have a couple of questions regarding to running the pipeline from bam files. 1) is there a way to specify the cell barcode and UMI labels or are they assumed to be CB and UB? and 2) what is the format of the sample sheet to run multiple bams?

Thanks

[lingminhao]

Hi @mcortes-lopez ,

• if I understand what you meant correctly, you want to create a new conda environment for your project that will use this pipeline. This nextflow pipeline is already containerized, so all required softwares is included in the singularity image you have pulled. However, you have to use lingminhao/bambusc:beta1.2 instead .
• If there is no barcode/UMI information on the read name (usually in BC_UMI$READNAME format) or they are not tagged as BC or UG in the bam files for every read, you can still specify the associated cell barcode and UMIs to every read using .tsv or .csv file format with three columns Read Name | Barcode | UMI and provide the path to this file under the --barcode_map argument in the pipeline
• You can find the format of the sample sheet under the --bams argument in the Required arguments section here

[mcortes-lopez]

Hi @lingminhao thanks for the quick answer. I was just testing the bambusc:beta1.2 and I got an error related to not being able to find utilityFunctions.R (attached my log here). I see that this script is present in the nexflow img download but it is not clear to me why it does not recognize it.

nextflow_bambu.log

[lingminhao]

Hi @mcortes-lopez ,

sorry for the late response, I was on a trip this week.
I looked into your log file. There is one possibility I can think of. Now you are running nextflow within the working directory /gpfs/commons/groups/landau_lab/mariela/CRC_project/bambu_test/. However, the directory where the nextflow pipeline is pulled is at /gpfs/commons/home/mcorteslopez/. By right, the volume is only mounted starting from the path where the nextflow github is pulled. So you would have to work at the directory after /gpfs/commons/home/mcorteslopez/ but not /gpfs/commons/groups/....

Let me know if this works.

Best Regards,
Min Hao

[mcortes-lopez]

Hi @lingminhao , thanks for looking into this! Indeed I tried running it in my home directory and it worked. Is there any work around to run the pipeline without having to be restricted to the directory where the singularity container is?

Best,
Mariela

[lingminhao]

Hi @mcortes-lopez,

A temporary work around for this would be to clone this nextflow pipeline directly to your working directory, then run the pipeline by replacing GoekeLab/bambu-singlecell-spatial with bambu-singlecell-spatial/main.nf.

Best Regards,
Min Hao