Benchmarking #118
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Benchmarking #118
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nictru
requested changes
May 13, 2024
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nictru
requested changes
Jul 15, 2024
modules/local/benchmarking/location_plots/templates/create_plots.py
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…Pearson-correllation. Implemented collection of correlation values.
…tion was calculated from the wrong files
…sometimes apear the wrong way round
…ecessary inputs after the merge
Fabian-Boehm
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nictru
requested changes
Sep 5, 2024
| label "process_single" | ||
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| conda "bioconda::seaborn=0.11.2" | ||
| container 'uphl/seaborn' |
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Use Seqera containers for creating Docker and singularity containers here
| container 'uphl/seaborn' | ||
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| input: | ||
| tuple val(id), path(bedfile1), path(bedfile2) |
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What id is inserted here? Should this not be called meta? If so, you can add the meta.id as a tag
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| input: | ||
| tuple val(meta), path(bed) | ||
| path "versions.yml" |
| label "process_single" | ||
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| conda "bioconda::seaborn=0.11.2" | ||
| container 'uphl/seaborn' |
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Use Seqera containers for creating Docker and singularity containers here
| @@ -0,0 +1,17 @@ | |||
| process OVERLAP_PLOT { | |||
| label "process_single" | |||
| def read_bed_file(file_path): | ||
| data = {'chromosome': [], 'start': [], 'strand': []} | ||
| with open(file_path, 'r') as file: | ||
| reader = csv.reader(file, delimiter='\t') |
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| conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" | ||
| container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0' |
| "description": "Run the pipeline in benchmarking mode.", | ||
| "default": false, | ||
| "fa_icon": "fas fa-chart-line", | ||
| "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare performance." |
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Suggested change
| "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare performance." | |
| "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare results." |
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| ch_versions = ch_versions.mix(SORT.out.versions) | ||
| ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) | ||
| ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) | ||
| ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) | ||
| ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions) | ||
| ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) | ||
| ch_versions = ch_versions.mix(AVERAGE_TSV.out.versions) | ||
| ch_versions = ch_versions.mix(OVERLAP_PLOT.out.versions) | ||
| ch_versions = ch_versions.mix(OVERLAP_JSON.out.versions) | ||
| ch_versions = ch_versions.mix(LOCATION_PLOT.out.versions) | ||
| ch_versions = ch_versions.mix(LOCATION_JSON.out.versions) | ||
| ch_versions = ch_versions.mix(SEQ_DEPTH_CORRELLATION.out.versions) | ||
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| ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) | ||
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| ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_JSON.out.report) | ||
| ch_reports = ch_reports.mix(OVERLAP_JSON.out.report) | ||
| ch_reports = ch_reports.mix(CORRELATION_MULTIQC.out.report) |
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Better move this mix operations to the locations where each tool is called instead of having one big junk
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Implementation of benchmarking and statistics based on the comparison of polyA selected RNA and total RNA