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task rmats { |
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task rmats { |
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String sample_id |
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String sample_id |
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File b1_txt |
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File b2_txt |
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File b1_1 |
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File b1_2 |
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File b1_3 |
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File b2_1 |
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File b2_2 |
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File b2_3 |
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File reference_gtf_file |
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File reference_gtf_file |
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mkdir -p ${sample_id}/output |
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mkdir -p ${sample_id}/output |
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mkdir -p ${sample_id}/tmp_output |
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mkdir -p ${sample_id}/tmp_output |
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python /usr/local/bin/rmats.py --b1 ${b1_txt} \ |
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--b2 ${b2_txt} \ |
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python /usr/local/bin/rmats.py --b1 ${b1_1},${b1_2},${b1_3} \ |
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--b2 ${b2_1},${b2_2},${b2_3}\ |
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--gtf ${reference_gtf_file} \ |
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--gtf ${reference_gtf_file} \ |
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-t paired \ |
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-t paired \ |
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--readLength 150 \ |
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--readLength 150 \ |