CI
94b5f2024b
Build pipeline: viash-hub.rnaseq.multiple-fixes-tnlvp
Source commit: e14b535c3b
Source message: update arguments
26 lines
569 B
Bash
26 lines
569 B
Bash
#!/bin/bash
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set -eo pipefail
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prefix_forward="forward"
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prefix_reverse="reverse"
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if [ $par_strandedness == 'reverse' ]; then
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prefix_forward="reverse"
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prefix_reverse="forward"
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fi
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bedtools genomecov \
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-ibam $par_bam \
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-bg \
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-strand + \
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$par_extra_bedtools_args | bedtools sort > $prefix_forward.bedGraph
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bedtools genomecov \
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-ibam $par_bam \
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-bg \
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-strand - \
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$par_extra_bedtools_args | bedtools sort > $prefix_reverse.bedGraph
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mv $prefix_forward.bedGraph $par_bedgraph_forward
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mv $prefix_reverse.bedGraph $par_bedgraph_reverse
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