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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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Add fasta and multifasta to readme #149

Closed erinyoung closed 1 year ago

erinyoung commented 1 year ago

It is possible to read in fasta and multifasta files via a sample sheet, but this hasn't made it to the readme.

In general, if the input isn't a paired-end set of fastq files, the fastq_2 column becomes what type it is, be it single reads (designated with 'single'), fasta files (designated with 'fasta'), or multifasta files (designated with 'multifasta'). It is important to note that the 'sample' column is not taken into account when the input in a multifasta file, but it still needs to exist.

sample,fastq_1,fastq_2
SRR13957125,/home/eriny/sandbox/test_files/cecret/reads/SRR13957125_1.fastq.gz,/home/eriny/sandbox/test_files/cecret/reads/SRR13957125_2.fastq.gz
SRR13957170,/home/eriny/sandbox/test_files/cecret/reads/SRR13957170_1.fastq.gz,/home/eriny/sandbox/test_files/cecret/reads/SRR13957170_2.fastq.gz
SRR13957177S,/home/eriny/sandbox/test_files/cecret/single_reads/SRR13957177_1.fastq.gz,single
SRR13957177F,/home/eriny/sandbox/test_files/cecret/fastas/SRR13957177.fasta,fasta
NA,/home/eriny/sandbox/test_files/cecret/multifasta/multifasta.fasta,multifasta
erinyoung commented 1 year ago

Should be resolved in https://github.com/UPHL-BioNGS/Cecret/pull/157