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nf-core_modules/tests/modules/fgbio/callmolecularconsensusreads/test.yml

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New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
- name: fgbio callmolecularconsensusreads
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/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
tags:
- fgbio
Update and check tests are running for all modules (#420) * Fixes for PR 371 * Fix tags * Add md5sum * Add md5sums for stringtie * Fix tests for modules where subtool = build * Fix pytest_software name conflicts * Change _ to / in test.yml tags * Nope...that didnt work * Fix sequenzautils/bam2seqz tests
2021-04-09 12:47:05 +00:00
- fgbio/callmolecularconsensusreads
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
files:
- path: output/fgbio/test_molreads.bam
Updated container versions for fgbio (#1878) * Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads * Corrected fgbio call container, trying to fix fgbio group tests * Removed incorrect line
2022-07-14 11:51:34 +00:00
md5sum: 6ae57429e3218f5eba9555d597b7c60f
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
- path: output/fgbio/test_out.bam
md5sum: d84e28fecc90c0752c543e934f10aa31
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