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Benchmarking #118
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Benchmarking #118
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Good start :)
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
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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" |
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Versions input?
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
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process OVERLAP_PLOT { | |||
label "process_single" |
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Add tag directive
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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Reminder
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Reminder
conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" | ||
container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0' |
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Reminder
"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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"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." |
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
Implementation of benchmarking and statistics based on the comparison of polyA selected RNA and total RNA