CI
a7b0d33a32
Build pipeline: viash-hub.biobox.main-2k68h
Source commit: aa43543e1f
Source message: Rseqc innerdistance (#159)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* full component with two tests
* fix default values
* adjust argument names and container image
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Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
25 lines
1.0 KiB
Bash
25 lines
1.0 KiB
Bash
#!/bin/bash
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set -exo pipefail
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inner_distance.py \
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-i $par_input_file \
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-r $par_refgene \
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-o $par_output_prefix \
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${par_sample_size:+-k "${par_sample_size}"} \
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${par_lower_bound:+-l "${par_lower_bound}"} \
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${par_upper_bound:+-u "${par_upper_bound}"} \
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${par_step:+-s "${par_step}"} \
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${par_mapq:+-q "${par_mapq}"} \
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> stdout.txt
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if [[ -n $par_output_stats ]]; then head -n 2 stdout.txt > $par_output_stats; fi
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[[ -n "$par_output_dist" && -f "$par_output_prefix.inner_distance.txt" ]] && mv $par_output_prefix.inner_distance.txt $par_output_dist
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[[ -n "$par_output_plot" && -f "$par_output_prefix.inner_distance_plot.pdf" ]] && mv $par_output_prefix.inner_distance_plot.pdf $par_output_plot
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[[ -n "$par_output_plot_r" && -f "$par_output_prefix.inner_distance_plot.r" ]] && mv $par_output_prefix.inner_distance_plot.r $par_output_plot_r
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[[ -n "$par_output_freq" && -f "$par_output_prefix.inner_distance_freq.txt" ]] && mv $par_output_prefix.inner_distance_freq.txt $par_output_freq
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exit 0 |