CI
6df312e701
Build pipeline: viash-hub.biobox.gatk-applybqsrspark-jpq6r
Source commit: c4ea23a0f5
Source message: Add RSEM prepare reference component (#89)
* initial commit
* incorporaate some requested changes
* update test
* change argument reference_fasta_files to multiple true and update docker setup
* Update src/rsem/rsem_prepare_reference/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/rsem/rsem_prepare_reference/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/rsem/rsem_prepare_reference/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* set multiple true
* update changelog
* Apply suggestions from code review
* fix script
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
23 lines
586 B
Bash
23 lines
586 B
Bash
#!/usr/bin/env bash
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set -eo pipefail
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unset_if_false=( par_rna par_strandedness par_tab par_bed_out par_name par_name_only par_split par_full_header )
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for par in ${unset_if_false[@]}; do
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test_val="${!par}"
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[[ "$test_val" == "false" ]] && unset $par
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done
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bedtools getfasta \
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-fi "$par_input_fasta" \
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-bed "$par_input_bed" \
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${par_rna:+-rna} \
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${par_name:+-name} \
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${par_name_only:+-nameOnly} \
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${par_tab:+-tab} \
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${par_bed_out:+-bedOut} \
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${par_strandedness:+-s} \
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${par_split:+-split} \
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${par_full_header:+-fullHeader} > "$par_output"
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