nf-core_modules/tests/modules/prokka/test.yml

- name: prokka
  command: nextflow run ./tests/modules/prokka -entry test_prokka -c ./tests/config/nextflow.config -c ./tests/modules/prokka/nextflow.config
  tags:
    - prokka
  files:
    - path: output/prokka/test/test.err
      md5sum: b3daedc646fddd422824e2b3e5e9229d
    - path: output/prokka/test/test.faa
      md5sum: a4ceda83262b3c222a6b1f508fb9e24b
    - path: output/prokka/test/test.ffn
      md5sum: 80f474b5367b7ea5ed23791935f65e34
    - path: output/prokka/test/test.fna
      md5sum: 787307f29a263e5657cc276ebbf7e2b3
    - path: output/prokka/test/test.fsa
      md5sum: 71bbefcb7f12046bcd3263f58cfd5404
    - path: output/prokka/test/test.gff
      md5sum: 5dbfb8fcf2db020564c16045976a0933
    - path: output/prokka/test/test.tbl
      md5sum: d8f816a066ced94b62d9618b13fb8add
    - path: output/prokka/test/test.tsv
      md5sum: da7c720c3018c5081d6a70b517b7d450
    - path: output/prokka/test/test.txt
      md5sum: b40e485ffc8eaf1feacf8d79d9751a33
    # Contain time stamps
    - path: output/prokka/test/test.gbk
    - path: output/prokka/test/test.log
    - path: output/prokka/test/test.sqn
add prokka module (#298) * add prokka module * adjust test outputs * fix prokka command * adjust test outputs * handle optional input * update pytest * update pytest * adjust test outputs * adjust test outputs * switch to lists for optional inputs, add md5sums for non-timestamped outputs * add optional prodigal training file * add optional prodigal training info to meta yaml 2021-03-23 09:51:23 +00:00			`- name: prokka`
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/prokka -entry test_prokka -c ./tests/config/nextflow.config -c ./tests/modules/prokka/nextflow.config`
add prokka module (#298) * add prokka module * adjust test outputs * fix prokka command * adjust test outputs * handle optional input * update pytest * update pytest * adjust test outputs * adjust test outputs * switch to lists for optional inputs, add md5sums for non-timestamped outputs * add optional prodigal training file * add optional prodigal training info to meta yaml 2021-03-23 09:51:23 +00:00			`tags:`
			`- prokka`
			`files:`
			`- path: output/prokka/test/test.err`
			`md5sum: b3daedc646fddd422824e2b3e5e9229d`
			`- path: output/prokka/test/test.faa`
			`md5sum: a4ceda83262b3c222a6b1f508fb9e24b`
			`- path: output/prokka/test/test.ffn`
			`md5sum: 80f474b5367b7ea5ed23791935f65e34`
			`- path: output/prokka/test/test.fna`
			`md5sum: 787307f29a263e5657cc276ebbf7e2b3`
			`- path: output/prokka/test/test.fsa`
			`md5sum: 71bbefcb7f12046bcd3263f58cfd5404`
			`- path: output/prokka/test/test.gff`
			`md5sum: 5dbfb8fcf2db020564c16045976a0933`
			`- path: output/prokka/test/test.tbl`
			`md5sum: d8f816a066ced94b62d9618b13fb8add`
			`- path: output/prokka/test/test.tsv`
			`md5sum: da7c720c3018c5081d6a70b517b7d450`
			`- path: output/prokka/test/test.txt`
			`md5sum: b40e485ffc8eaf1feacf8d79d9751a33`
			`# Contain time stamps`
			`- path: output/prokka/test/test.gbk`
			`- path: output/prokka/test/test.log`
			`- path: output/prokka/test/test.sqn`