Missing output/ intermediary files

[lauratwomey]

Hi! Thank you so much for your hard work on this pipeline - it's really good!

I have a few questions regarding the outputs:

1. Certain output files that you mention in the main github page are missing from the results/ folder, is there a way to get the pipeline to output them? I've had a quick look with find . -name *config_stats.jason but I could not find it in the work directory either. I couldn't see any relevant parameter to get intermediary files in the documentation. These files are missing and would be really useful to me!

   • ./fastq_ingress_results/reads/{{ alias }}.fastq.gz
   • ./{{ alias }}/config_stats.json
   • ./{{ alias }}/read_summary.tsv

2. Regarding the ./{{ alias }}/tagged.bam file, is this already filtered for duplicates? If so, how could I access the .bam file with all reads?

Thank you so much!

Some more info:

• I'm using v2.0.3 and everything ran smoothly.
• params.yml custom params: expected_cells: 1000 kit_name: '3prime' kit_version: 'v3' full_length_only: false matrix_min_genes: 5

[nrhorner]

HI @lauratwomey

Thanks for your question,

1. The ./fastq_ingress_results/reads/{{ alias }}.fastq.gz entry should not be in the README. These were never planned to be output as they are just the concatenated input reads and would increase the already large amount of disk space the workflow requires.

./{{ alias }}/config_stats.json was inadvertently removed from a previous version and will be replaced in the next release (expect that in the next couple of days).

./{{ alias }}/read_summary.tsv The file this is referring to is actually called read_tags.tsv. This should have been renamed, sorry for the confusion.

2. The BAM file is not filtered for duplicates and contains all reads taht were assigned a barcode.

Hope this helps,

Thanks,

Neil

[lauratwomey]

Thanks a million Neil! Extremely helpful. Looking forward to the next release then:)

[lauratwomey]

Hi again Neil - I've pulled the latest release and rerun the pipeline but the config_stats.json is still not outputed?

[nrhorner]

Hi @lauratwomey

I just ran v2.1.0 and output/<alias>/config_stats.json was there for me. Can you check your version please?

[nrhorner]

Closing through lack of response