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Does Cookiercutter support zipped fastq sequences as input? #25

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catiajose7 opened this issue Jul 31, 2019 · 0 comments

catiajose7 commented Jul 31, 2019

I tried a lot of things, such as

R1_i=$MY_PATH/"$SAMPLE_ID_M"_S"$POP_M"_L001_R1_001"$TEST".fastq.gz
R2_i=$MY_PATH/"$SAMPLE_ID_M"_S"$POP_M"_L001_R2_001"$TEST".fastq.gz

R1=$(zcat $R1_i)
R2=$(zcat $R2_i)

cookiecutter extract -1 "$R1" -2 "$R2" -t "$THREADS" -f "$MSK" -o "$OUTPUT_MSR"

It appeared: "Argument list too long"
If there is a way to do it can give me an example.

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