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@ -52,4 +52,72 @@ process QUALIMAP_BAMQC {
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qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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"""
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mkdir -p $prefix/css
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mkdir $prefix/images_qualimapReport
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mkdir $prefix/raw_data_qualimapReport
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cd $prefix/css
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touch agogo.css
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touch basic.css
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touch bgtop.png
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touch comment-close.png
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touch doctools.js
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touch down-pressed.png
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touch jquery.js
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touch plus.png
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touch qualimap_logo_small.png
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touch searchtools.js
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touch up.png
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touch websupport.js
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touch ajax-loader.gif
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touch bgfooter.png
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touch comment-bright.png
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touch comment.png
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touch down.png
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touch file.png
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touch minus.png
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touch pygments.css
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touch report.css
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touch underscore.js
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touch up-pressed.png
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cd ../images_qualimapReport/
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touch genome_coverage_0to50_histogram.png
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touch genome_coverage_quotes.png
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touch genome_insert_size_across_reference.png
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touch genome_mapping_quality_histogram.png
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touch genome_uniq_read_starts_histogram.png
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touch genome_coverage_across_reference.png
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touch genome_gc_content_per_window.png
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touch genome_insert_size_histogram.png
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touch genome_reads_clipping_profile.png
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touch genome_coverage_histogram.png
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touch genome_homopolymer_indels.png
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touch genome_mapping_quality_across_reference.png
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touch genome_reads_content_per_read_position.png
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cd ../raw_data_qualimapReport
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touch coverage_across_reference.txt
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touch genome_fraction_coverage.txt
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touch insert_size_histogram.txt
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touch mapped_reads_nucleotide_content.txt
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touch coverage_histogram.txt
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touch homopolymer_indels.txt
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touch mapped_reads_clipping_profile.txt
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touch mapping_quality_across_reference.txt
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touch duplication_rate_histogram.txt
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touch insert_size_across_reference.txt
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touch mapped_reads_gc-content_distribution.txt
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touch mapping_quality_histogram.txt
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cd ../
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touch genome_results.txt
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touch qualimapReport.html
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cd ../
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
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END_VERSIONS
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"""
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}
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