fetchngs
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nf-core
Pipeline to fetch metadata and raw FastQ files from public databases
Version `2.5` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
### Description of feature This will allow using Tower Datasets with the pipeline as only tsv / csv is currently supported.
### Description of the bug It is now over a month that I handle my data with `fetchngs` and I am pretty satisfied with the results. However, I recently encountered...
### Description of feature We should try to strip out the custom Python scripts I initially wrote for this pipeline. They have worked relatively well but are fragile to breakages...
### Description of feature Running: ``` nextflow run nf-core/fetchngs -r 1.7 --input list.txt --outdir sra -profile docker ``` Pipeline fails at `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO`: ```text [ERROR] The server couldn't fulfill the request....
### Description of feature I would like to request for the ability to pass in our dbGAP credentials through the --ngc flag of SRAtools so as to be able to...
First pass implementation to use [`ffq`](https://github.com/pachterlab/ffq#usage) to fetch metadata from public databases.
GEO support was stripped out in v1.7. See [this PR](https://github.com/nf-core/fetchngs/pull/102) for more information. We should add it back in when we have a robust solution.
### Description of feature Hi nfcore/fetchngs team, It would be awesome to add --save_merged_fastq for merging technical repeats to fetchngs. Would be very useful for downstream programs that cant deal...
### Description of the bug Test run on the minimal dataset failed ### Command used and terminal output ```console Command nextflow run nf-core/fetchngs -profile test docker Output Core Nextflow options...
