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nf-core_modules/tests/modules/bismark/genomepreparation/test.yml

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Fix version commands (#749) * Fix version commands * Fix version commands: again
2021-09-27 21:10:37 +00:00
- name: bismark genomepreparation test workflow
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
add bismark/genome_preparation + tests
2021-02-18 09:56:36 +00:00
tags:
- bismark
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
- bismark/genomepreparation
add bismark/genome_preparation + tests
2021-02-18 09:56:36 +00:00
files:
Fixing vcftools and bismark tests (#383) * fixed vcftools * fixed genomepreparation, methylationextractor * fixed deduplicate
2021-03-25 09:12:08 +00:00
- path: ./output/bismark/BismarkIndex/genome.fasta
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
md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
md5sum: 6c4f549575e5882ff3a97ae10ae2e7be
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
md5sum: 10a8854e5eeb95629f46d24b0d8da70c
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
md5sum: bc5d407e6fce3e1cdb4b23ab2a20f707
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
md5sum: 48bf400de85cd7324fbf6bf38fe2dc95
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
md5sum: d37d586b41b6a36efb25839961d242cb
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
md5sum: 17f51e65f44477962226a83b369b2bc4
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
md5sum: d36044c5dfe37af0411f60d446585bc6
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
md5sum: e529375ec2039112161465b5169fcd59
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
md5sum: b1e855685ed634daa7df8e180c9b2fc4
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
md5sum: a6fa4068ed10872568f32568c66cb600
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
md5sum: fc5b634e2f5137801e3801d62ad05f74
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
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