SRA NBCI fetch and preprossing script only works automatically for illumina sequences #40
Description
using fmalmeida/ngs-preprocess:v2.6
nextflow should identify sequencing platform and route preprocessing to nanopore/pacbio/illumina.
ERROR ~ Error executing process > 'SRA_FETCH:GET_FASTQ (SRR9641620)'
Caused by:
Process `SRA_FETCH:GET_FASTQ (SRR9641620)` terminated with an error exit status (3)
Command executed:
fasterq-dump \
--include-technical \
--split-files \
--threads 2 \
--outdir ./SRR9641620_data \
--progress \
SRR9641620
Command exit status:
3
Command output:
(empty)
Command error:
2024-05-09T13:37:02 fasterq-dump.3.0.3 err: accession 'SRR9641620' is PACBIO, please use fastq-dump instead
fasterq-dump quit with error code 3