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‎tests/start_from_recalibration.nf.test.snap

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{
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"-profile test --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null": {
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"content": [
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{
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"CREATE_INTERVALS_BED": {
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"gawk": "5.1.0"
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"GATK4_INTERVALLISTTOBED": {
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"gatk4": "4.6.1.0"
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},
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"INDEX_CRAM": {
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"samtools": 1.21
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},
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"MOSDEPTH": {
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"mosdepth": "0.3.10"
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},
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"SAMTOOLS_STATS": {
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"samtools": 1.21
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},
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"TABIX_BGZIPTABIX_INTERVAL_COMBINED": {
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"tabix": 1.21
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},
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},
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[
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"csv",
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"csv/recalibrated.csv",
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"multiqc",
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"multiqc/multiqc_data",
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"multiqc/multiqc_data/BETA-multiqc.parquet",
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"multiqc/multiqc_data/llms-full.txt",
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"multiqc/multiqc_data/mosdepth-coverage-per-contig-single.txt",
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"multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt",
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"multiqc/multiqc_data/mosdepth_cov_dist.txt",
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"multiqc/multiqc_data/mosdepth_cumcov_dist.txt",
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"multiqc/multiqc_data/mosdepth_perchrom.txt",
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"multiqc/multiqc_data/multiqc.log",
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"multiqc/multiqc_data/multiqc_citations.txt",
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"multiqc/multiqc_data/multiqc_data.json",
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"multiqc/multiqc_data/multiqc_general_stats.txt",
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"multiqc/multiqc_data/multiqc_samtools_stats.txt",
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"multiqc/multiqc_data/multiqc_software_versions.txt",
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"multiqc/multiqc_data/multiqc_sources.txt",
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"multiqc/multiqc_data/samtools-stats-dp.txt",
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"multiqc/multiqc_data/samtools_alignment_plot.txt",
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"multiqc/multiqc_plots",
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"multiqc/multiqc_plots/pdf",
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"multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-cnt.pdf",
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"multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-pct.pdf",
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"multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf",
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"multiqc/multiqc_plots/pdf/samtools-stats-dp.pdf",
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"multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf",
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"multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf",
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"multiqc/multiqc_plots/png",
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"multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-cnt.png",
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"multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-pct.png",
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"multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png",
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"multiqc/multiqc_plots/png/samtools-stats-dp.png",
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"multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png",
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"multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png",
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"multiqc/multiqc_plots/svg",
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"multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg",
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"multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg",
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"multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg",
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"multiqc/multiqc_plots/svg/samtools-stats-dp.svg",
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"multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg",
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"multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg",
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"multiqc/multiqc_report.html",
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"pipeline_info",
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"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
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"preprocessing",
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"reference"
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"preprocessing/recalibrated",
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"preprocessing/recalibrated/test",
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"preprocessing/recalibrated/test/test.recal.cram",
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"preprocessing/recalibrated/test/test.recal.cram.crai",
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"reference",
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"reports",
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"reports/mosdepth",
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"reports/mosdepth/test",
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"reports/mosdepth/test/test.recal.mosdepth.global.dist.txt",
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"reports/mosdepth/test/test.recal.mosdepth.region.dist.txt",
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"reports/mosdepth/test/test.recal.mosdepth.summary.txt",
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"reports/mosdepth/test/test.recal.regions.bed.gz",
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"reports/mosdepth/test/test.recal.regions.bed.gz.csi",
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"reports/samtools",
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"reports/samtools/test",
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"reports/samtools/test/test.recal.cram.stats"
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],
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[
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"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
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"mosdepth-coverage-per-contig-single.txt:md5,115b9a93bcf511419e6622919172f321",
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"mosdepth-cumcoverage-dist-id.txt:md5,df2fc825dfc41e30f72f5d125a6447ee",
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"mosdepth_perchrom.txt:md5,115b9a93bcf511419e6622919172f321",
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"multiqc_citations.txt:md5,6239b0f0a9736ccaf3baff3014dd585b",
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"samtools-stats-dp.txt:md5,c8deaa643c44fd800cbf14ac35fb7719",
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"samtools_alignment_plot.txt:md5,8908b56b3040f2c53b15591adf93a266",
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"test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972",
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"test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
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"test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
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"test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
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"test.recal.regions.bed.gz.csi:md5,b3716e5cd1744610e69c29bd4ffad259"
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],
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"No BAM files",
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"No CRAM files",
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[
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"test.recal.cram:md5,463ac3b905fbf4ddf113a94dbfa8d69f"
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],
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"No VCF files"
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-12T16:53:05.463394899"
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"timestamp": "2025-08-18T11:44:29.232705858"
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},
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"-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --skip_tools baserecalibrator --tools strelka": {
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"content": [

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