2021-02-17 11:34:51 -05:00
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- name: Run qualimap bamqc test workflow
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2021-07-07 05:10:18 -04:00
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command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
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2021-02-17 11:34:51 -05:00
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tags:
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- qualimap
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2021-04-08 04:10:52 -04:00
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- qualimap/bamqc
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2021-02-17 11:34:51 -05:00
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files:
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Converge test data usage (#249)
* initial data restructuing
* fixed bedtools_complement
* fixed bedtools_genomecov
* fixed bedtools_getfasta
* fixed bedtools_intersect
* fixed bedtools maskfasta
* fixed bedtools_merge
* fixed bedtools_slop
* fixed bedtools_sort
* fixed bismark_genome_preparation
* fixed blast
* fixed bowtie data
* fixed bowtie2 data
* fixed bwa data
* fixed bwamem2 data usage
* fixed cat_fastq data
* fixed cutadapt data
* fixed dsh data
* fixed fastp data
* fixed fastqc; fixed bug with wrong fastq format
* fixed gatk
* fixed data for gffread, gunzip
* fixed ivar paths
* fixed data paths for minimap2
* fixed mosdepth
* fixed multiqc, pangolin
* fixed picard data paths
* fixed data paths for qualimap, quast
* fixed salmon data paths
* fixed samtools paths
* fixed seqwish, stringtie paths
* fixed tabix, trimgalore paths
* cleaned up data
* added first description to README
* changed test data naming again; everything up to bwa fixed
* everything up to gatk4
* fixed everything up to ivar
* fixed everything up to picard
* everything up to quast
* everything fixed up to stringtie
* switched everyting to 'test' naming scheme
* fixed samtools and ivar tests
* cleaned up README a bit
* add (simulated) methylation test data
based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90
* bwameth/align: update data paths and checksums
also, build index on the go
* bwameth/index: update data paths and checksums
* methyldackel/extract: update data paths and checksums
* methyldackel/mbias: update data paths and checksums
* bismark/deduplicate: update data paths and checksums
* remove obsolete testdata
* remove empty 'dummy_file.txt'
* update data/README.md
* methyldackel: fix test
* Revert "methyldackel: fix test"
This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a.
* methyldackel: fix test
for real
* move test.genome.sizes
* changed test names
* switched genomic to genome and transcriptome
* fix bedtools, blast
* fix gtf, tabix, .paf
* fix bowtie,bwa,bwameth
* fixed: bwa, bwamem, gatk, gffread, quast
* fixed bismark and blast
* fixed remaining tests
* delete bam file
Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 05:10:57 -05:00
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- path: ./output/qualimap/test/qualimapReport.html
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- path: ./output/qualimap/test/genome_results.txt
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md5sum: 00ad697dbec5141428ac8d850c13e1c5
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- path: ./output/qualimap/test/css/plus.png
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md5sum: 0125e6faa04e2cf0141a2d599d3bb220
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- path: ./output/qualimap/test/css/down-pressed.png
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md5sum: ebe8979581eda700fb234a73c661a4b9
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- path: ./output/qualimap/test/css/underscore.js
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md5sum: db5ba047a66617d4cd3e8c5099cc51db
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- path: ./output/qualimap/test/css/ajax-loader.gif
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md5sum: ae6667053ad118020b8e68ccf307b519
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- path: ./output/qualimap/test/css/searchtools.js
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md5sum: d550841adeedc8ed47c40ee607620937
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- path: ./output/qualimap/test/css/up.png
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- path: ./output/qualimap/test/css/file.png
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- path: ./output/qualimap/test/css/up-pressed.png
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- path: ./output/qualimap/test/css/down.png
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- path: ./output/qualimap/test/css/minus.png
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- path: ./output/qualimap/test/css/bgtop.png
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- path: ./output/qualimap/test/css/comment.png
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- path: ./output/qualimap/test/css/basic.css
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md5sum: 25b2823342c0604924a2870eeb4e7e94
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- path: ./output/qualimap/test/css/report.css
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md5sum: 7a5f09eaf7c176f966f4e8854168b812
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- path: ./output/qualimap/test/css/pygments.css
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md5sum: d625a0adb949f181bd0d3f1432b0fa7f
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- path: ./output/qualimap/test/css/comment-close.png
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- path: ./output/qualimap/test/css/doctools.js
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md5sum: 5ff571aa60e63f69c1890283e240ff8d
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- path: ./output/qualimap/test/css/comment-bright.png
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- path: ./output/qualimap/test/css/qualimap_logo_small.png
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- path: ./output/qualimap/test/css/websupport.js
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md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
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- path: ./output/qualimap/test/css/agogo.css
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md5sum: bd757b1a7ce6fdc0288ba148680f4583
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- path: ./output/qualimap/test/css/bgfooter.png
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- path: ./output/qualimap/test/css/jquery.js
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md5sum: 10092eee563dec2dca82b77d2cf5a1ae
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- path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
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md5sum: 749630484c5b24b4973ad613d85a2341
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- path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
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md5sum: dbcb28c1ab2f0c78f6e803a24a2a695f
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- path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
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md5sum: d5ba8feb5418091d6e00e4ad0c865cf1
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- path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
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md5sum: 8b638330338758c156200a37602c53d5
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- path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
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md5sum: dc553f58b5e361b9e5c894f118347bc1
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- path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
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md5sum: f57a631c72f2373ca4d3f6c8deb1ad6d
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- path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
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md5sum: 42223637499a2221cf99b4dd08badb6f
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- path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
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md5sum: c7c7db9fa3febd58b27e95cff857df90
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- path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
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md5sum: ba7484d97ab505ab8642d73074afef04
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- path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
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md5sum: 7875c892eb75a6da5115b10e3b2b767e
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- path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
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md5sum: fbabd3fea386712fa453e7c9825107af
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- path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
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md5sum: e199f6930d4bda5f9e871cb5c628a69a
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- path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
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- path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png
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