nf-core
fetchngs pipeline not working on scRNAseq
Hi there!
I have used fetchngs with no problems for downloading RNAseq data from SRA. However, when I tried the same with scRNAseq data from SRA. The pipeline ended saying "Pipeline completed successfully-", but when I opened the results folder, it had the "IDS_NOT_DOWNLOADED.txt" containing the input IDs. This was tried with the following script;
#!/bin/bash #SBATCH --time=24:00:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=8 #SBATCH --mem=4gb #SBATCH --job-name=ids8-download #SBATCH --error=job.%J.err #SBATCH --output=job.%J.out #SBATCH --partition=tmp_anvil,batch
module load nextflow module load singularity
The job command(s):
nextflow run nf-core/fetchngs --input ids8.txt -profile singularity
nextflow run nf-core/fetchngs --input ids8.txt -profile singularity
This was tried on following SRA Id's SRX7278088 SRX7278087 SRX7278086 SRX7278085 SRX7278084 SRX7278083 SRX7278082 SRX7278081
Can anybody troubleshoot this and provide a way to make it work.
UPDATE: The fetchngs pipeline does not seem to work on any other datasets besides RNASeq. Tested pipeline on exome sequencing datasets and single-cell RNAsequencing datasets. It does not download datasets, but completes the job saying it has successfully completed the pipeline from execution.
regards Arch
I just tried this with your input and it seems to download the files just fine. Was this also your experience?
Closing as unable to reproduce. We also added explicit support for 10x data in https://github.com/nf-core/fetchngs/issues/144 which should hopefully fix the issue. Please feel free to re-open or create a separate issue if the problem persists.
