* 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>
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
* Update functions.nf for publish_by_id
* Pass a list of publish_by_id instead of a string
* Remove NF version
* Rename code linting file
* Run separate workflow for nf-core modules lint
* Adjust nf-core update comment
* Comment out linting from pytest-workflow.yml
* Remove commented out linting code from pytest-workflow.yml
* Adjust spacing
* Adjust spacing again
* Move NF version to job level for linting
* Add CAPSULE_LOG none env when installing NF
* Remove NXF_ANSI_LOG env for linting
* Revert changes
* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feature: add new issue template for creating new module
* Apply suggestions from code review
* Apply suggestions from code review
Co-authored-by: Kevin Menden <kevin.menden@live.com>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
* initial data restructuing
* fixed bedtools_complement
* fixed bedtools_genomecov
* fixed bedtools_getfasta
* fixed bedtools_intersect
* fixed bedtools maskfasta
* fixed bedtools_merge
* fixed bedtools_slop
* fixed bedtools_sort
* fixed bismark_genome_preparation
* fixed blast
* fixed bowtie data
* fixed bowtie2 data
* fixed bwa data
* fixed bwamem2 data usage
* fixed cat_fastq data
* fixed cutadapt data
* fixed dsh data
* fixed fastp data
* fixed fastqc; fixed bug with wrong fastq format
* fixed gatk
* fixed data for gffread, gunzip
* fixed ivar paths
* fixed data paths for minimap2
* fixed mosdepth
* fixed multiqc, pangolin
* fixed picard data paths
* fixed data paths for qualimap, quast
* fixed salmon data paths
* fixed samtools paths
* fixed seqwish, stringtie paths
* fixed tabix, trimgalore paths
* cleaned up data
* added first description to README
* changed test data naming again; everything up to bwa fixed
* everything up to gatk4
* fixed everything up to ivar
* fixed everything up to picard
* everything up to quast
* everything fixed up to stringtie
* switched everyting to 'test' naming scheme
* fixed samtools and ivar tests
* cleaned up README a bit
* add (simulated) methylation test data
based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90
* bwameth/align: update data paths and checksums
also, build index on the go
* bwameth/index: update data paths and checksums
* methyldackel/extract: update data paths and checksums
* methyldackel/mbias: update data paths and checksums
* bismark/deduplicate: update data paths and checksums
* remove obsolete testdata
* remove empty 'dummy_file.txt'
* update data/README.md
* methyldackel: fix test
* Revert "methyldackel: fix test"
This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a.
* methyldackel: fix test
for real
* move test.genome.sizes
* changed test names
* switched genomic to genome and transcriptome
* fix bedtools, blast
* fix gtf, tabix, .paf
* fix bowtie,bwa,bwameth
* fixed: bwa, bwamem, gatk, gffread, quast
* fixed bismark and blast
* fixed remaining tests
* delete bam file
Co-authored-by: phue <patrick.huether@gmail.com>
