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

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Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- name: plasmidid
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/plasmidid -entry test_plasmidid -c ./tests/config/nextflow.config -c ./tests/modules/plasmidid/nextflow.config
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
tags:
- plasmidid
files:
- path: output/plasmidid/test/data/database_reconstruct_test.length
md5sum: a57c401f27ae5133823fb09fb21c8a3c
- path: output/plasmidid/test/data/test.coverage_adapted_clustered_ac
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/plasmidid/test/data/test.err
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: 011108fd8b0bb4a4c0b5b2cf46452a90
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/data/test.fna
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: 503a5e1d4654bb2df19420e211070db3
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/data/test.gbk
- path: output/plasmidid/test/data/test.gff
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/data/test.karyotype_individual.txt
md5sum: aaf0f5bfe297fb9846ace761ff018d22
- path: output/plasmidid/test/data/test.karyotype_summary.txt
md5sum: aaf0f5bfe297fb9846ace761ff018d22
- path: output/plasmidid/test/data/test.plasmids.blast
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: 241045ea62156c1ca9bc1eb734ac9526
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/data/test.plasmids.blast.links
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: a44d6aa388b582da8ad53c5b49467b8f
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/data/test.plasmids.complete
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: fbc7235285dbb963b07561dd6972a883
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/database/test.fna
md5sum: 6b843fe652b4369addb382f61952c3dd
- path: output/plasmidid/test/database/test.gbk
- path: output/plasmidid/test/database/test.gff
md5sum: 7e65da147d0a413020b0d92b7b03ffcd
- path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta
FIx plasmidid tests for new contigs.fasta file (#438) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes
2021-04-13 07:49:44 +00:00
md5sum: 8a8537dd3b21e6905f9367b51c3b3074
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
- path: output/plasmidid/test/images/test_individual.circos.conf
md5sum: f74467ab77232e2b342e2bd408897b12
- path: output/plasmidid/test/images/test_MT192765.1_individual.circos.conf
md5sum: 548443ba0a68065a69383fe32b226780
- path: output/plasmidid/test/images/test_summary.circos.conf
md5sum: e59dc3b77ee610a48b79230da705aba0
- path: output/plasmidid/test/images/test_MT192765.1.png
- path: output/plasmidid/test/images/test_summary.png
- path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.clusters.tab
md5sum: cf75e4418631796bb4675129b575915d
- path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta
md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
- path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta.blast.tmp.ndb
md5sum: f67f8be1e00eb7d3512869071fb4c2c2
- path: output/plasmidid/test/kmer/database.filtered_0.8_term.fasta
md5sum: c7fe0e9e9a94d98d7f85a7be99c032fd
- path: output/plasmidid/test/kmer/database.filtered_0.8_term.mash.distances.tab
md5sum: fd5408c3c2f8f68dc01e0123bb6a9079
- path: output/plasmidid/test/logs/draw_circos_images.log
- path: output/plasmidid/test/logs/plasmidID.log
- path: output/plasmidid/test/test_final_results.html
- path: output/plasmidid/test/test_final_results.tab
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