CI
1e77c47f20
Build pipeline: viash-hub.biobox.qualimap-nmgj2
Source commit: 58d7dacfc2
Source message: Update src/qualimap/qualimap_rnaseq/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
73 lines
2.6 KiB
Bash
73 lines
2.6 KiB
Bash
#!/bin/bash
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## VIASH START
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## VIASH END
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[[ "$par_tar" == "false" ]] && unset par_tar
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[[ "$par_force" == "false" ]] && unset par_force
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[[ "$par_quiet" == "false" ]] && unset par_quiet
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[[ "$par_restart" == "false" ]] && unset par_restart
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[[ "$par_auto_lineage" == "false" ]] && unset par_auto_lineage
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[[ "$par_auto_lineage_euk" == "false" ]] && unset par_auto_lineage_euk
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[[ "$par_auto_lineage_prok" == "false" ]] && unset par_auto_lineage_prok
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[[ "$par_augustus" == "false" ]] && unset par_augustus
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[[ "$par_long" == "false" ]] && unset par_long
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[[ "$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition
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[[ "$par_miniprot" == "false" ]] && unset par_miniprot
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tmp_dir=$(mktemp -d -p "$meta_temp_dir" busco_XXXXXXXXX)
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prefix=$(openssl rand -hex 8)
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busco \
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--in "$par_input" \
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--mode "$par_mode" \
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--out "$prefix" \
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--out_path "$tmp_dir" \
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--opt-out-run-stats \
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${meta_cpus:+--cpu "${meta_cpus}"} \
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${par_lineage_dataset:+--lineage_dataset "$par_lineage_dataset"} \
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${par_augustus:+--augustus} \
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${par_augustus_parameters:+--augustus_parameters "$par_augustus_parameters"} \
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${par_augustus_species:+--augustus_species "$par_augustus_species"} \
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${par_auto_lineage:+--auto-lineage} \
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${par_auto_lineage_euk:+--auto-lineage-euk} \
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${par_auto_lineage_prok:+--auto-lineage-prok} \
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${par_contig_break:+--contig_break $par_contig_break} \
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${par_datasets_version:+--datasets_version "$par_datasets_version"} \
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${par_e_value:+--evalue "$par_e_value"} \
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${par_force:+--force} \
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${par_limit:+--limit "$par_limit"} \
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${par_long:+--long} \
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${par_metaeuk:+--metaeuk} \
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${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \
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${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \
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${par_miniprot:+--miniprot} \
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${par_quiet:+--quiet} \
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${par_restart:+--restart} \
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${par_scaffold_composition:+--scaffold_composition} \
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${par_tar:+--tar} \
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out_dir=$(find "$tmp_dir/$prefix" -maxdepth 1 -name 'run_*')
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if [[ -n "$par_short_summary_json" ]]; then
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cp "$out_dir/short_summary.json" "$par_short_summary_json"
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fi
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if [[ -n "$par_short_summary_txt" ]]; then
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cp "$out_dir/short_summary.txt" "$par_short_summary_txt"
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fi
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if [[ -n "$par_full_table" ]]; then
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cp "$out_dir/full_table.tsv" "$par_full_table"
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fi
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if [[ -n "$par_missing_busco_list" ]]; then
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cp "$out_dir/missing_busco_list.tsv" "$par_missing_busco_list"
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fi
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if [[ -n "$par_output_dir" ]]; then
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if [[ -d "$par_output_dir" ]]; then
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rm -r "$par_output_dir"
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fi
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cp -r -L "$out_dir" "$par_output_dir"
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fi
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