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nf-core_modules/tests/modules/seqtk/subseq/test.yml

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Feat seqtk update (#503) * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Replaced functions.nf in seqtk/subseq * Refreshed tests for sample and subseq * Corrected paired-end test and YAML description for sample Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-14 07:23:15 -04:00
- name: seqtk subseq test_seqtk_subseq
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 02:58:40 -05:00
command: nextflow run ./tests/modules/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/subseq/nextflow.config
Feat seqtk update (#503) * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Replaced functions.nf in seqtk/subseq * Refreshed tests for sample and subseq * Corrected paired-end test and YAML description for sample Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-14 07:23:15 -04:00
tags:
- seqtk
- seqtk/subseq
files:
- path: output/seqtk/genome.fasta.filtered.fa.gz
md5sum: 488001c0fbedabf24d3e10fe7f96c78a
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