Mercurial > repos > petr-novak > re_utils

comparison test_run1.sh @ 5:378565f5a875 draft

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author petr-novak
date Fri, 22 Nov 2019 07:56:48 -0500
parents a4cd8608ef6b
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4:d397f5a85464 5:378565f5a875
7 7
8 echo "single fastq filtering with defaults" 8 echo "single fastq filtering with defaults"
9 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test1.fasta -G tmp/test1.png -c 10 -N 0 9 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test1.fasta -G tmp/test1.png -c 10 -N 0
10 10
11 echo "single fastq filtering with with sampling" 11 echo "single fastq filtering with with sampling"
12 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.fasta -G tmp/test2.png -c 10 -N 0 -n 500 12 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2a.fasta -G tmp/test2a.png -c 10 -N 0 -n 500
13
14 echo "single fastq filtering with with sampling"
15 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2b.fasta -G tmp/test2b.png -c 10 -N 0 -n 647
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17 echo "single fastq filtering with with sampling"
18 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2c.fasta -G tmp/test2c.png -c 10 -N 0 -n 839
19
20 echo "single fastq filtering with with sampling"
21 ./single_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2d.fasta -G tmp/test2d.png -c 10 -N 0 -n 911
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13 23
14 echo "single fastq filtering with contaminant removing" 24 echo "single fastq filtering with contaminant removing"
15 ./single_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -a test_data/ERR215189_1_part.fastq.gz -o tmp/test3.fasta -G tmp/test3.png -c 10 -N 0 25 ./single_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -a test_data/ERR215189_1_part.fastq.gz -o tmp/test3.fasta -G tmp/test3.png -c 10 -N 0
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17 27