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I'm trying to use fetchngs in part of a reproducib...
# fetchngs
m
I'm trying to use fetchngs in part of a reproducibility refactor, and I'm encountering issues with just retrieving the data through fetchngs. There are around 3000 accessions, and most come back with information from the SRA however there are some that come back without it. The SRA_IDS_TO_RUNINFO succeeds, but the tsv only has the header line, and then when it gets to SRA_RUNINFO_TO_FTP it errors because the 2nd tsv file isn't written out even though the python script "succeeds". Checking these accessions, there is information in both ENA and SRA on them, but the pipeline isn't populating the runinfo.tsv. What action should I take?
m
Are you using dev or the latest release?
m
Copy code
export NXF_SYNTAX_PARSER=v1
WORKFLOW=nf-core/fetchngs
nextflow run "${WORKFLOW}" \
    -r 1.12.0 \
    -params-file params.yml \
    -profile "${NXF_PROFILE:-apptainer}" \
    ${CLI_OPTS:-""}
m
Can you try dev, it might be an issue that is fixed already
m
It seems like the runinfo is all populated this time. Can you or someone then make a release to include these bug fixes. The last release was something like 2 years ago
m
That's the plan
Evangelos put me to it
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