2021-03-22 16:46:11 +00:00
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- name: Run bismark_genomepreparation test workflow
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command: nextflow run ./tests/software/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
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2021-02-18 09:56:36 +00:00
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tags:
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- bismark
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2021-03-22 16:46:11 +00:00
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- bismark_genomepreparation
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2021-02-18 09:56:36 +00:00
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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 10:10:57 +00:00
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- path: ./output/bismark/BismarkIndex/test_genome.fasta
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md5sum: 6e9fe4042a72f2345f644f239272b7e6
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
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md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
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md5sum: 6c4f549575e5882ff3a97ae10ae2e7be
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
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md5sum: 10a8854e5eeb95629f46d24b0d8da70c
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
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md5sum: 4ed93abba181d8dfab2e303e33114777
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
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md5sum: bc5d407e6fce3e1cdb4b23ab2a20f707
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
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md5sum: 48bf400de85cd7324fbf6bf38fe2dc95
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
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md5sum: d37d586b41b6a36efb25839961d242cb
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
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md5sum: 17f51e65f44477962226a83b369b2bc4
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
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md5sum: d36044c5dfe37af0411f60d446585bc6
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
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md5sum: e529375ec2039112161465b5169fcd59
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
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md5sum: b1e855685ed634daa7df8e180c9b2fc4
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
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md5sum: a6fa4068ed10872568f32568c66cb600
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
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md5sum: fc5b634e2f5137801e3801d62ad05f74
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- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
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md5sum: 4ed93abba181d8dfab2e303e33114777
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