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Description
Hi, thank you for this great work!
I am working with small RNA sequencing data, my command is as follows:
echo "umi_tools extract --bc-pattern='.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)' --extract-method='regex' --quality-encoding=phred33 --quality-filter-threshold=20 -I test_raw.fastq.gz -S test_extract.fastq -L test_extract.log" | rush -k 'echo "{}"'
result:
umi_tools extract --bc-pattern='.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.test_extract.log)(?P<discard_2>.*)' --extract-method='regex' --quality-encoding=phred33 --quality-filter-threshold=20 -I test_raw.fastq.gz -S test_extract.fastq -L test_extract.log
"{12}" to "test_extract.log", because: {n}, nth field in delimiter-delimited data. (Same in GNU parallel)
but we want (do nothing with the input):
umi_tools extract --bc-pattern='.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)' --extract-method='regex' --quality-encoding=phred33 --quality-filter-threshold=20 -I test_raw.fastq.gz -S test_extract.fastq -L test_extract.log
So, how to output {12} directly ?
Thanks in advance!