These edits enable "prep_subs.py" to identify if a FASTQ is paired-end or single-end. If the FASTQ is single-end, the name of the R1 FASTQ file will be entered into the "fastq_2" column of "input.tsv". The "bam.smk" and "qc.smk" pipelines are then able to detect this and the files are processed as single-end in the "fastqs_to_ubam" rule and in the "fastqc" rule. This will allow for streamlined processing of single-end and paired-end FASTQs together without error.
These edits enable "prep_subs.py" to identify if a FASTQ is paired-end or single-end. If the FASTQ is single-end, the name of the R1 FASTQ file will be entered into the "fastq_2" column of "input.tsv". The "bam.smk" and "qc.smk" pipelines are then able to detect this and the files are processed as single-end in the "fastqs_to_ubam" rule and in the "fastqc" rule. This will allow for streamlined processing of single-end and paired-end FASTQs together without error.