2 commits

Author	SHA1	Message	Date
Harshil Patel	20d8250d9f	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
Edmund Miller	669fb5caed	Homer Modules (#75) ... * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21a * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>	2021-09-08 15:40:34 +00:00