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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
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/bismark/genomepreparation/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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