combined quantification output from psirc

[jpfry327]

Description of the bug

Hi, I've run the pipeline with default parameters, and I believe the main execution has worked. However, I have a question about the output in the 4_quantification folder. When I look at the combined output from psirc, I get an empty circular.tsv file (in 4_quantification/psirc/combined). From what I understand, this file is created by finding the circular transcript abundances from the individual samples. In my case, I have individual sample abundances at, for example, 4_quantification/psirc/samples/siCONTROL_REP1/psirc/siCONTROL_REP1. When I inspect the abundance.tsv file at this location, I see abundances for transcripts such as "chr1:2191529-2192844:-", which I'm assuming are the circRNA transcripts. So the pipeline has quantified circRNAs for my individual samples, but it looks like they have not been combined.

Looking through the code, it looks like you use awk to extract transcripts starting with "circ_". But it looks like none of the transcripts start with "circ_", but are of the form "chr1:2191529-2192844:-"?

Anyway, regardless of the empty output at 4_quantification/psirc/combined, can I just manually combine all the files at 4_quantification/psirc/samples/*/psirc/*/abundance.tsv? Or does the combination step do any additional processing?

Command used and terminal output

nextflow run nf-core/circrna -r dev \
    -profile nu_genomics \
    -resume \
    --outdir nextflow_dir \
    --input samplesheet.csv \
    --gtf ~/ylab/jfp0082/ref/gencode.v42.annotation.gtf \
    --fasta ~/ylab/jfp0082/ref/hg38.fa \
    --bowtie2 "/home/jfp0082/ylab/jfp0082/ref/bowtie2" \
    --igenomes_ignore \
    --genome null

Relevant files

No response

System information

No response

[nictru]

This should be fixed now, feel free to re-open if you encounter this again

[pnolabs]

Dear @nictru,

I believe I encounter the same issue. The file circular.tsv at '4_quantification/psirc/combined' is empty. Even though I see abundances for transcripts such as "chr1:766328-774280:-" besides "ENST00000832828.1" etc. at '4_quantification/psirc/samples/Sample1/psirc/Sample1'.

Could you please point me in the right direction on how to proceed from there? Is manually combining all the files at '4_quantification/psirc/samples//psirc//abundance.tsv' an option?

I also found a mismatch between my .command.sh file and the current nf-core/circrna GitHub version (modules/local/quantification/split_types/main.nf). Mine use awk to extract transcripts starting with "circ_". The GitHub version "^.+:[0-9]+-[0-9]+(:[+-])?".

Command used

nextflow run nf-core/circrna -r dev \
    -profile apptainer \
    -resume \
    -c /scripts/circRNA/nxt.config \
    -params-file /scripts/circRNA/params.yml \
    --input /01_data/circRNA/samplesheet.csv \
    --outdir /02_analysis/circRNA/output \
    --phenotype /01_data/circRNA/phenotype.csv

EDIT: I think I figured it out. I had an older cached copy of the pipeline. Deleted the old. And re-pulled the dev pipeline. 'modules/local/quantification/split_types/main.nf' is now updated.