Commit graph

287 commits

Author SHA1 Message Date
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
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* 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
2021-07-07 10:10:18 +01:00
Kevin Menden
2395734492
Adapt linting action (#556)
* bump bcftools filter

* fix bcftools

* adapt module linting
2021-07-02 14:15:32 +02:00
Edmund Miller
bdee7804ca
build: Bump version to 21.04.0 (#481)
* build: Bump version to 21.04.0

Recent stable release https://github.com/nextflow-io/nextflow/releases/tag/v21.04.0

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 00:38:29 +01:00
Harshil Patel
f34892c1af
Test PR for nf-core modules lint (#414)
* 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
2021-04-09 07:58:43 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389)
* 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>
2021-04-08 09:10:52 +01:00
Edmund Miller
6e4b23a1ca
ci: Upload work directory on failure (#388)
Closes #374
2021-03-25 09:34:19 +00:00
Edmund Miller
1fc4aa260d
ci: Add 21.03.0 version to matrix (#317) 2021-03-22 22:57:59 +00:00
Gregor Sturm
bed31cd9b4
Add link to issue in pull request template (#312)
* Add link to issue in pull request template

* Update PULL_REQUEST_TEMPLATE.md
2021-03-22 10:04:20 -07:00
Maxime Garcia
e61f400167
feature: add new issue template for creating new module (#283)
* 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>
2021-03-19 15:39:22 +01:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml

* Change filters.yml name

* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main (#270)
* 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
2021-03-15 12:16:43 +00:00
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary (#260)
* fix: update and sort filters

* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 14:45:46 +01:00
Kevin Menden
4566525da2
Converge test data usage (#249)
* 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>
2021-03-04 10:10:57 +00:00
Maxime Garcia
ea6fde0193
Merge pull request #252 from MaxUlysse/master_tiddit
New module: tiddit
2021-02-25 09:34:33 +01:00
MaxUlysse
f62196a4a6 feat: add tiddit_sv module 2021-02-24 15:59:10 +01:00
FriederikeHanssen
48d6d88104
Update .github/filters.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-02-24 10:29:13 +01:00
FriederikeHanssen
4673c119c7 resolve merge conflicts 2021-02-24 10:03:16 +01:00
Jose Espinosa-Carrasco
8f4363ccb5
Merge pull request #247 from JoseEspinosa/bcftools-mpileup
Add bcftools mpileup module
2021-02-24 09:24:43 +01:00
Harshil Patel
5287fe5f95
Merge pull request #245 from phue/bismark_deduplicate
add bismark/deduplicate + tests
2021-02-23 21:08:24 +00:00
Harshil Patel
4703a60443
Merge pull request #220 from phue/bwameth
add bwameth modules
2021-02-23 21:01:54 +00:00
JoseEspinosa
20bcb00ea0 Fix indentation 2021-02-23 19:08:56 +01:00
JoseEspinosa
4b3c86ed9f Add tests for bcftools-mpileup 2021-02-23 19:05:57 +01:00
phue
e73bda26f5 add bismark/deduplicate + tests 2021-02-23 18:02:16 +01:00
Gregor Sturm
38349417ad
Update .github/workflows/pytest-workflow.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-23 14:14:29 +01:00
Gregor Sturm
94bdc62123 Only use one thread for pytest-workflow
This avoids a race condition on the conda cache.
2021-02-23 14:06:52 +01:00
FriederikeHanssen
a0c9777d60 add seqkit to GHA 2021-02-23 12:43:30 +01:00
kevinmenden
3fee38ee2d added gatk4 revertsam 2021-02-22 15:21:39 +01:00
kevinmenden
bd585265ce added entry to filters.yml 2021-02-22 13:36:49 +01:00
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs 2021-02-19 14:11:30 +01:00
MaxUlysse
2bf3890afb Merge remote-tracking branch 'upstream/master' into master_tiddit 2021-02-19 13:37:45 +01:00
kevinmenden
3ac5c5fad6 working test 2021-02-19 13:36:42 +01:00
kevinmenden
c0693fa3db remove whitespace 2021-02-19 13:30:40 +01:00
Kevin Menden
5c325f2942
Merge branch 'master' into master 2021-02-19 13:08:43 +01:00
kevinmenden
bd8ba42a8d added gatk4 SamToFastq 2021-02-19 12:41:29 +01:00
kevinmenden
6dcaf5ffc8 add gatk4 bedtointervallist 2021-02-19 11:26:31 +01:00
MaxUlysse
eaff4eb0ff fix: order alphabetically 2021-02-19 10:56:04 +01:00
phue
0d8f5f0572 add bismark/genome_preparation + tests 2021-02-18 10:56:36 +01:00
Patrick Hüther
dba295155e
Merge pull request #219 from phue/qualimap_bamqc
add qualimap/bamqc + test
2021-02-18 10:09:03 +01:00
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel
add methyldackel modules
2021-02-17 22:17:26 +00:00
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish
Add module for seqwish/induce
2021-02-17 22:14:49 +00:00
phue
52b00d4286 add methyldackel/mbias + tests 2021-02-17 19:27:57 +01:00
phue
5ad7c6bc51 add methyldackel/extract + tests + testdata 2021-02-17 19:18:55 +01:00
phue
84a5da0d91 add bwameth/align module + tests 2021-02-17 18:23:11 +01:00
Michael L Heuer
206b605666 Add module for seqwish/induce 2021-02-17 11:19:47 -06:00
phue
180b1cf36b add bwameth/index module + test 2021-02-17 18:03:48 +01:00
phue
b5b259a2d9 add qualimap/bamqc + test 2021-02-17 17:34:51 +01:00
phue
a156bdfc03 faidx: add filter 2021-02-17 17:01:22 +01:00
Maxime Garcia
842173be9f
Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE
fix: add guidelines to PRs and issues
2021-02-17 00:36:35 +01:00
MaxUlysse
ebb6d5de1f fix: Apply suggestions from code review 2021-02-17 00:34:55 +01:00