nf-core / nf-core/funcprofiler
CAT_FASTQ: symlink fastq files when no merging needed
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Description
Description of feature
Related to #69, I had a look at the CAT_FASTQ output. Most of my files have just one set of fastqs per sample so the cat step unecessarily duplicates data.
Maybe this process can be updated to check if there are only 1 fastq in each of the input1 and input2 folders, and if so, just symlink the file to the output instead. Might need to symlink from the original fastq path rather than symlink the working dir fastq symlink.
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with the CAT_FASTQ process and related issue #69, then trace how the input1 and input2 folders and output paths are constructed. Confirm the behavior for one FASTQ per input folder and for multiple FASTQs; done means the single-file case produces symlinks without merging while the existing multi-file behavior remains unchanged.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100