Harshil Patel
5e18e36895
Update and check tests are running for all modules ( #420 )
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* Fixes for PR 371
* Fix tags
* Add md5sum
* Add md5sums for stringtie
* Fix tests for modules where subtool = build
* Fix pytest_software name conflicts
* Change _ to / in test.yml tags
* Nope...that didnt work
* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
Florian Wuennemann
0f53c3b96b
Added kallistobustools/ref ( #408 )
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* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me
* Removed trailing whitespace line 29
* Moved workflow from meta to options.
* Update main.nf
* Forgot to remove previous testing input channel for workflow.
* Apply suggestions from code review
Applied changes suggested by @drpatelh
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added gtf to meta.yml.
* Apply suggestions from code review
Adding @drpatelh suggested changes.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Moved workflow to input value. Fixed tests.
* Update tests/software/kallistobustools/ref/test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 09:41:41 +01:00
Yuk Kei Wan
16e8d21477
Nanoplot and sequencing_summary.txt for Nanopore test data ( #364 )
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* add nanoplot
* add Nanopore 100 read subset bam and fastq
* add nanoplot module and sequencing_summary.txt
* Update pytest_software.yml
* Update main.nf
* test directory path
* testing one output file
* Update main.nf
* fix typo
* remove path to test outputs (it worked locally)
* use test_data.config in test
* add meta.yml
* allowing either summary.txt or fastq.gz inputs
* fix linting and test.yml
* test whether github check can catch the output
* add summary.txt test output paths
* check Nanoplot-report.html output
2021-04-09 08:31:38 +01:00
Anthony Underwood
63b3975292
Update gubbins module to use new files ( #417 )
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* new gubbins module
* new gubbins module
* new gubbins module
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* Update tests/config/test_data.config
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
* new snpsites module
* new snpsites module
* new snpsites module
* new snpsites module
* adding fasttree module
* correct trailing whitespace
* using sarscov2 as a test dir
* use sars-cov-2 alignment
* remove old test alignment
* new snpsites module
* new snpsites module
* new snpsites module
* updated test file names
* new snpsites module
* remove snpsites from gubbins branch
* remove redundant test_fas alignment
* update md5 sums
Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco
f90dde0d88
Add plasmidid module ( #410 )
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* 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 22:44:30 +01:00
Anthony Underwood
be390a25e5
adding fasttree module ( #412 )
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* adding fasttree module
* correct trailing whitespace
* using sarscov2 as a test dir
* remove TODO
* update test data naming
* further test data naming updates
* remove options in favour of $options.args
* ensure non standard exit codes don't cause an issue
* update md5sum
2021-04-08 18:15:23 +01:00
avantonder
710ab76b90
new module: gubbins ( #377 )
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* new gubbins module
* new gubbins module
* new gubbins module
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gubbins/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* new gubbins module
* Update tests/config/test_data.config
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/gubbins/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new gubbins module
* new gubbins module
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-07 16:31:24 +01:00
Robert A. Petit III
c9256616b9
update tests for new config ( #384 )
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* update tests for new config
* fix quast, update more
* more updates!
* more tests updated
* fix tests, added tabix gff3.gz
* Delete main.nf
Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:22:06 +01:00
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz ( #395 )
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* added files
* edited files
* removed file
* README.md edited
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 07:08:27 +02:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data ( #386 )
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* Adding tar.gz kraken2 db to test data
* Update test path files for untar module
* Update test path files for kraken2/run module
* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests ( #365 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
* Initial commit for test data config
* Rename test data
* Include test config
* Update indents
* Update test for FastQC via config
* Remove quotes of bottom-level variables
* Use underscores in key names
* Get tests working for fastp
* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Yuk Kei Wan
323856a9da
add nanopore 100-read test subset (fast5, fastq, and bam/bai) ( #344 )
2021-03-24 05:13:34 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) ( #302 )
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* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Update pytest_software.yml
* Update main.nf
* fix linting error
* Delete test.yml
* Create functions.nf
* Update main.nf
* change test data
* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) ( #301 )
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* Adding in optitype prototype (To be worked on these days)
* I've tried my best 😆
* No idea
* Add in YML stuff
* Fix paths
* Ok, lets try this
* Adding proper options
* Replacec configbuilder thing
* Fix seq_type
* Adding human bam - sarscov doesnt work
* Fix a bunch of things
* -def
* Make this test run
* Fancy as fuck
* Update tests/software/optitype/test.yml
* Add proper tag
* Remove md5sums
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
yocra3
569ff03af9
Add readgroup to bam files ( #324 )
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* Add readgroup to bam files
Add recalibration table
* Solve README.md issue
2021-03-23 11:59:49 +01:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module ( #173 )
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* Normal bam file added
* Normal bam.bai file added
* Tumour bam bai files added
* human dir added
* annotation dir added
* cnvkit dir added
* cnvkit dir added
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* changed input filenames
* edited main.nf
* edited main.nf
* edited meta.nf
* edited test.yml
* filters.yml
* edited main
* edited main
* edited meta
* edited meta
* edited main
* removed unwanted lines
* edited the path to the main.nf
* removed function.nf
* added functions.nf
* deleted 2 workflows and craeted a common workflow
* deleted paths for 2 workflows and created paths for a common workflow
* Deleted annotation dir
* deleted params.modules
* Edited meta.with_normal
* deleted normal_280_sub_chr21.bam
* deleted normal_280_sub_chr21.bam.bai
* deleted tumour_278_sub_chr21.bam
* deleted tumour_278_sub_chr21.bam.bai
* Edited input and script parts
* Edited input part
* Added
* Edited args
* Edited script
* Edited input
* Changed annotation to annotationfile
* Changed description of the tool
* edited singularuty container
* edited input
* line 44 removed trailing whitespace
* Edited addParams
* Deleted pdf output
* Deleted pdf output
* edited the path to main.nf
* edited path to the main.nf
* Added docker image version
* Removed extra ../
* added md5sums
* added md5sums
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Edited the script
* Edited the input
* Edited main.nf
* Edited main.nf
* edited md5sum for reference.cnn
* removed human fasta
* removed human fasta.fai
* added GRCh38 fasta
* added GRCh38 fasta.fai
* added hg19 fasta.fai
* added hg19 fasta
* Edited fasta file name
* Edited bed file names and md5sums
* Edited md5sums
* edited the input and script section
* edited input section
* added targetfile
* changed the files
* changed the output files
* added bam files
* added bam files
* remove files
* added md5sums
* replace file
* added files
* edited tests/software/cnvkit files
* edited tests/software/cnvkit files
* edited authors list
* removed files
* added files
* added files
* added files
* added files
* added file
* added file
* added file
* added file
* edited files
* edited files
* edited files
* edited files
* edited files
* edited files
* added new module
* added new module
* edited files
* edited file
* edited file
* edited file
* removed files
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Jose Espinosa-Carrasco
313241749c
Add kraken2 run module ( #266 )
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* Add kraken2 run module
* Add kraken2 run module
* Add coronavirus kraken2 db
* Adding kraken2 run tests
* Update software/kraken2/run/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixing files commited by mistake
* Remove params for meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
Kevin Menden
a90332906b
add mergebamalignment ( #259 )
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* add mergebamalignment
* fix test.yml
* update to latest gatk4 version
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/data/README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/meta.yml
* fixed unmapped/unaligned
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
a552d97849
Exchange VCF data by sarscov2 data ( #261 )
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* added sarscov2 vcf data; adjusted bcftools tests
* updated README.md
* deleted old VCF files; fixed mergevcfs
* fixed tabix
2021-03-09 10:04:08 +01:00
Kevin Menden
4566525da2
Converge test data usage ( #249 )
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* 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
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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
Harshil Patel
50b98d56a1
Merge pull request #246 from drpatelh/master
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Update iVar modules
2021-02-24 13:00:05 +00:00
Harshil Patel
5287fe5f95
Merge pull request #245 from phue/bismark_deduplicate
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add bismark/deduplicate + tests
2021-02-23 21:08:24 +00:00
Harshil Patel
4703a60443
Merge pull request #220 from phue/bwameth
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add bwameth modules
2021-02-23 21:01:54 +00:00
drpatelh
aaaef7df8c
Add BAM index
2021-02-23 20:42:16 +00:00
phue
e73bda26f5
add bismark/deduplicate + tests
2021-02-23 18:02:16 +01:00
kevinmenden
43446bc37e
added sarscov2 fastq and bam files
2021-02-22 13:19:12 +01:00
kevinmenden
bb5c0ceca5
adding SplitNCigarReads
2021-02-19 14:59:29 +01:00
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs
2021-02-19 14:11:30 +01:00
kevinmenden
02abe106ec
added optional reference dictionary as input
2021-02-19 14:09:32 +01:00
kevinmenden
6dcaf5ffc8
add gatk4 bedtointervallist
2021-02-19 11:26:31 +01:00
phue
a963c67481
bwameth: pass genome index as directory
...
instead of single files
2021-02-18 11:51:36 +01:00
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel
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add methyldackel modules
2021-02-17 22:17:26 +00:00
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
Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant
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Add ivar variants
2021-02-16 23:20:30 +00:00
MaxUlysse
fa34f806d2
chores: add bgzip files for tests
2021-02-16 17:06:09 +01:00
Anders Goncalves da Silva
89f65e0875
Merge branch 'master' into ivar-variant
2021-02-15 20:50:35 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth
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Add mosdepth module
2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva
4af7414419
Add tests for ivar variants
2021-02-15 09:29:40 -08:00
JoseEspinosa
6e92a6a080
Adding mosdepth module
2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2
2021-02-15 13:08:52 +01:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim
2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge
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Add bcftools merge module
2021-02-12 23:20:30 +00:00
JoseEspinosa
5313698705
Add bcftools merge module
2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva
0a6e8400ac
Add reference SC2 genome to test data
2021-02-12 11:27:12 -08:00
MaxUlysse
0afddf6ca4
fix: CI is working
2021-02-12 15:24:09 +01:00
