CI
90a16ac646
Build pipeline: viash-hub.biobox.add-agat-convert-spgff2tsv-t5ds2
Source commit: fa5ed706e5
Source message: add tests
25 lines
884 B
Bash
25 lines
884 B
Bash
#!/bin/bash
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set -eo pipefail
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[[ "$par_nogroup" == "false" ]] && unset par_nogroup
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[[ "$par_bisulfite" == "false" ]] && unset par_bisulfite
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[[ "$par_reverse_compliment" == "false" ]] && unset par_reverse_compliment
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IFS=";" read -ra input <<< $par_input
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$(which falco) \
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${par_nogroup:+--nogroup} \
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${par_contaminants:+--contaminants "$par_contaminants"} \
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${par_adapters:+--adapters "$par_adapters"} \
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${par_limits:+--limits "$par_limits"} \
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${par_subsample:+-subsample $par_subsample} \
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${par_bisulfite:+-bisulfite} \
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${par_reverse_compliment:+-reverse-compliment} \
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${par_outdir:+--outdir "$par_outdir"} \
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${par_format:+--format "$par_format"} \
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${par_data_filename:+-data-filename "$par_data_filename"} \
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${par_report_filename:+-report-filename "$par_report_filename"} \
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${par_summary_filename:+-summary-filename "$par_summary_filename"} \
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${input[*]}
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