CI
aa043fdc19
Build pipeline: viash-hub.biobox.qualimap-6tqq7
Source commit: 28cd122935
Source message: Merge branch 'main' into qualimap
39 lines
1.3 KiB
Bash
39 lines
1.3 KiB
Bash
#!/bin/bash
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## VIASH START
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## VIASH END
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set -e
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[[ "$par_remove_dups" == "false" ]] && unset par_remove_dups
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[[ "$par_customized_index_file" == "false" ]] && unset par_customized_index_file
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[[ "$par_sparse" == "false" ]] && unset par_sparse
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[[ "$par_remove_overlaps" == "false" ]] && unset par_remove_overlaps
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# change the coverage input from X;X;X to X,X,X
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par_coverage=$(echo "$par_coverage" | tr ';' ',')
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samtools stats \
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${par_coverage:+-c "$par_coverage"} \
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${par_remove_dups:+-d} \
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${par_required_flag:+-f "$par_required_flag"} \
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${par_filtering_flag:+-F "$par_filtering_flag"} \
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${par_GC_depth:+--GC-depth "$par_GC_depth"} \
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${par_insert_size:+-i "$par_insert_size"} \
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${par_id:+-I "$par_id"} \
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${par_read_length:+-l "$par_read_length"} \
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${par_most_inserts:+-m "$par_most_inserts"} \
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${par_split_prefix:+-P "$par_split_prefix"} \
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${par_trim_quality:+-q "$par_trim_quality"} \
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${par_ref_seq:+-r "$par_ref_seq"} \
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${par_split:+-S "$par_split"} \
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${par_target_regions:+-t "$par_target_regions"} \
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${par_sparse:+-x} \
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${par_remove_overlaps:+-p} \
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${par_cov_threshold:+-g "$par_cov_threshold"} \
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${par_input_fmt_option:+-O "$par_input_fmt_option"} \
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${par_reference:+-R "$par_reference"} \
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"$par_input" \
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> "$par_output"
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exit 0 |