Enable download of files form 10X Genomics experiments #145
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maxulysse
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Apr 25, 2023
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| fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2,3,4}.fastq.gz' | ||
| def outfile = meta.single_end ? "${prefix}.fastq" : prefix | ||
| """ | ||
| export NCBI_SETTINGS="\$PWD/${ncbi_settings}" | ||
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| fasterq-dump \\ | ||
| $args \\ | ||
| --split-files \\ | ||
| --include-technical \\ |
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modules should be modified in nf-core modules, or patched in the pipeline.
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how is your PR coming from your |
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Hmm, it seems I only have a master branch in my private fork.... |
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Will be fixed in #146 |
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).We have previously opened an issue because, currently,
fetchngsfails to download data from 10X genomics experiments (#144). The issue in question has a lot more details of what goes wrong, and how to fix it.Changes
In essence, we have changed the following things (for the
PREFETCH_FASTERQDUMP_SRATOOLSworkflow only):--split-filesand--include-technicaltofasterq-dumpTests
We have carried out tests using single-end as well as paired-end files, both using the ENA (default) and SRATOOLS options; the pipelines and resulting files are all in working order, as before.
For a 10X genomics test dataset, the new version results in 3 output files (see #144 for additional details) using the SRATOOLS route. In ENA mode, only a single bulk (and meaningless) file is produced, as before.
I am afraid I am not able to add any meaningful CI tests (don't really know how to), but maybe you would be able to find a minimal test case that works?
NOTE:
We have not changed anything for the workflow downloading data from the ENA (which is the default of
fetchngs). The ENA does not serve out read that are marked as 'technical' at all, so all 10X Genomics data will appear as a single FastQ file - which means that the cell-ID and UMI read is missing. Thus, for 10X data you have to force downloads via thesratoolkitroute - or end up with one single, bulk file.Many thanks to @wzheng0520 for figuring this out, and the nf-core community for their constant support!