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nf-core_modules/tests/modules/bcftools/mpileup/test.yml

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update test data paths (#373) * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
- name: bcftools mpileup test_bcftools_mpileup
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/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
Add tests for bcftools-mpileup
2021-02-23 18:05:57 +00:00
tags:
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
- bcftools/mpileup
update test data paths (#373) * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
- bcftools
Add tests for bcftools-mpileup
2021-02-23 18:05:57 +00:00
files:
- path: output/bcftools/test.bcftools_stats.txt
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: 4bb496a523ce6b35432d3bbb6b24a885
update test data paths (#373) * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
- path: output/bcftools/test.vcf.gz.tbi
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: f5e9c86c2269138663c9fb3effe840da
update test data paths (#373) * update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
- path: output/bcftools/test.vcf.gz
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: f37c4bdb0b7a4330477d6716ae2778c2
Remove bcftools and ivar module customisations (#1217) * Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
2022-01-18 16:04:56 +00:00
- name: bcftools mpileup test_bcftools_save_mpileup
command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
tags:
- bcftools/mpileup
- bcftools
files:
- path: output/bcftools/test.bcftools_stats.txt
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: 4bb496a523ce6b35432d3bbb6b24a885
Remove bcftools and ivar module customisations (#1217) * Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
2022-01-18 16:04:56 +00:00
- path: output/bcftools/test.vcf.gz.tbi
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: f5e9c86c2269138663c9fb3effe840da
Remove bcftools and ivar module customisations (#1217) * Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
2022-01-18 16:04:56 +00:00
- path: output/bcftools/test.vcf.gz
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: f37c4bdb0b7a4330477d6716ae2778c2
Remove bcftools and ivar module customisations (#1217) * Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
2022-01-18 16:04:56 +00:00
- path: output/bcftools/test.mpileup
Bump tool versions for modules required in viralrecon (#1859) * Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
2022-07-07 13:48:04 +00:00
md5sum: d7c55262aa6637487ba1c621983cfb49
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