suzannejin
9115c12f88
new module: samtools/fastq ( #316 )
...
* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
2021-03-23 12:13:07 +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
Robert A. Petit III
c2aa95cb6c
add prokka module ( #298 )
...
* add prokka module
* adjust test outputs
* fix prokka command
* adjust test outputs
* handle optional input
* update pytest
* update pytest
* adjust test outputs
* adjust test outputs
* switch to lists for optional inputs, add md5sums for non-timestamped outputs
* add optional prodigal training file
* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
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
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 ( #311 )
...
* Inital nf-core create
* remove TODO comments, input and output files defined
* add get version in script
* added flow control for single/paired end data
* added script main commands
* removed completed TODO messages
* removed completed TODO messages
* added software info
* added input reads description
* added output description
* added description and keywords
* added single end test
* added paired end test
* fixed sample name flag
* fixed reverse read variable
* added test yaml
* update for pytest_software
* order in pytest_software was different
* replaced functions.nf with copy from another module
* simplify read command line
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Garcia
0a4fa5050a
Update main.nf ( #314 )
2021-03-22 17:16:43 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval ( #309 )
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* add adapterremoval module
* fix indentations
* switch to process_medium
* update docker tests
* remove duplicated entry
* fix line ending
* Update software/adapterremoval/main.nf
* Update software/adapterremoval/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
Jose Espinosa-Carrasco
cfa8f64c4f
Adding unicycler module ( #307 )
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* Adding unicycler module
* Do not forget to change default keywords on meta.yml
2021-03-22 18:14:24 +01:00
Patrick Hüther
7fe6f9fab2
bismark: remove underscores from process names ( #303 )
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* sanitize process names
no underscores allowed
* remove underscores from process names
2021-03-22 17:46:11 +01:00
Florian Wuennemann
592002aa23
add picard_collectwgsmetrics ( #304 )
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* Added new module picard/collectwgsmetrics.
* Removed unused outputs from meta.yml
* Added version.txt file back to meta.yml
* Updated test.yml
* Removed md5sum from test.yaml and added contain tests.
* Update functions.nf
Fixed missing newline formatting.
* Update main.nf
Fixed missing newline formatting.
* style(picard): Remove trailing whitespace
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 17:05:59 +01:00
Patrick Hüther
eb9178970f
add bismark/summary ( #295 )
...
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/summary
* remove md5sum check for bismark_summary_report.html
it contains a timestamp
* fix tests
* update meta.yml
* remove mysterious index files
2021-03-22 14:58:54 +01:00
Yuk Kei Wan
134c8ef6ce
add samtools merge ( #296 )
...
* add samtools merge
* Update pytest_software.yml
* get it back to 20.11.0-edge
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
2021-03-22 13:48:23 +01:00
Patrick Hüther
f9ce8664ba
add bismark/report ( #297 )
...
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/report
* fix test filepaths
* remove mysterious index files
2021-03-22 13:38:08 +01:00
Patrick Hüther
04704c2034
add bismark/methylation_extractor ( #274 )
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* add bismark/methylation_extractor
* add tests for bismark/methylation_extractor
* bismark/methylation_extractor: add genome_preparation to filters
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* remove params from meta.yml
* pytest: remove md5sum checks for gzipped output
gzip stores timestamps in the file header, so the checksum will be different each time
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Jose Espinosa-Carrasco
72e81d6e90
Add spades module ( #277 )
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* Add spades module
* Reorder gatk4 modules alphabetically
* Update software/spades/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
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
Harshil Patel
d1cb9a845f
Check for minimum NF version ( #278 )
2021-03-18 12:00:32 +01:00
Kevin Menden
a90332906b
add mergebamalignment ( #259 )
...
* 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
3c4d9466f4
Adding minia for viralrecon ( #267 )
...
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 12:54:15 +01:00
Kevin Menden
17dbff52f4
added gatk4 variantfiltration ( #265 )
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* added gatk4 variantfiltration
* replace merge with filter
* Update software/gatk4/variantfiltration/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* updated input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds ( #273 )
...
* Fix bowtie build test
* Forgot to delete old bowtie_build
* Fix bowtie2 build tests
* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
Maxime Garcia
66fd57a8bc
fix: update tiddit_sv tests ( #272 )
2021-03-15 14:02:20 +00:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
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* 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 )
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* 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
Kevin Menden
0218824b86
add task.cpus to pangolin ( #263 )
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* add task.cpus to pangolin
* bumped pangolin to v2.3.2
2021-03-10 09:02:23 +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
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary ( #260 )
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* 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
JoseEspinosa
155c2a1185
Check only for vcf file to exists (includes cmd)
2021-02-26 07:14:29 +01:00
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
FriederikeHanssen
4673c119c7
resolve merge conflicts
2021-02-24 10:03:16 +01:00
FriederikeHanssen
7627e656ee
Add all tests back in
2021-02-24 09:57:23 +01:00
FriederikeHanssen
8a7333c13b
lower case path
2021-02-24 09:53:11 +01:00
FriederikeHanssen
7f6e5d9ab5
try to make a single test pass on GHA, passes locally
2021-02-24 09:48:55 +01:00
Jose Espinosa-Carrasco
8f4363ccb5
Merge pull request #247 from JoseEspinosa/bcftools-mpileup
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Add bcftools mpileup module
2021-02-24 09:24:43 +01:00
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
b581bdc36c
Update test script
2021-02-23 20:43:05 +00:00
drpatelh
aaaef7df8c
Add BAM index
2021-02-23 20:42:16 +00:00
JoseEspinosa
e9d90007c5
Adding arguments to make md5 hashes stable
2021-02-23 19:39:24 +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
FriederikeHanssen
e67515809a
try to only make paired-end test work, pass locally with conda & docker
2021-02-23 15:47:16 +01:00
FriederikeHanssen
13733b2581
Add beautiful md5sums
2021-02-23 14:57:07 +01:00
FriederikeHanssen
5e365d5eff
Make all these tests pass
2021-02-23 14:09:46 +01:00
FriederikeHanssen
25a2a16f2d
Try to make a single test pass
2021-02-23 13:34:50 +01:00
FriederikeHanssen
312bf85f70
use reasonable option params
2021-02-23 11:26:54 +01:00
FriederikeHanssen
9c51e05125
remove wrong md5 sums
2021-02-23 11:25:45 +01:00
FriederikeHanssen
c7d2bc8d43
Add tests for different options
2021-02-23 11:14:51 +01:00
FriederikeHanssen
ec63f335d5
Add split2 options
2021-02-22 22:43:32 +01:00
kevinmenden
3fee38ee2d
added gatk4 revertsam
2021-02-22 15:21:39 +01:00
kevinmenden
efd60d94ee
adding revertsam/ fix typo in mergevcfs
2021-02-22 15:10:20 +01:00
kevinmenden
69d7bb4fca
reformatted input to tuple
2021-02-22 13:31:54 +01:00
kevinmenden
43446bc37e
added sarscov2 fastq and bam files
2021-02-22 13:19:12 +01:00
phue
2d8baa8b75
bwameth/index: update test.yml
2021-02-20 12:55:09 +01:00
phue
c67e591caf
apply suggestions from review
...
thanks @drpatelh
2021-02-20 12:51:01 +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
3ac5c5fad6
working test
2021-02-19 13:36:42 +01:00
kevinmenden
c288e081b4
initial commit adding mergevcfs
2021-02-19 13:29:08 +01:00
Kevin Menden
5c325f2942
Merge branch 'master' into master
2021-02-19 13:08:43 +01:00
kevinmenden
908e55ee5c
fixed tag
2021-02-19 12:46:59 +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
phue
a963c67481
bwameth: pass genome index as directory
...
instead of single files
2021-02-18 11:51:36 +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
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add qualimap/bamqc + test
2021-02-18 10:09:03 +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
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish
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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
1a414261c4
bwameth/align: update checksums
2021-02-17 18:35:39 +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
FriederikeHanssen
5f9aa7264e
Add tests
2021-02-17 17:25:41 +01:00
Patrick Hüther
0cbe0a4173
Update tests/software/samtools/faidx/main.nf
...
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
2021-02-17 17:24:50 +01:00
phue
3b1d126a0e
add samtools/faidx + tests
2021-02-17 16:46:34 +01:00
Harshil Patel
ed573db194
Merge pull request #184 from MaxUlysse/master_fix_ci
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fix: update checksum or filename
2021-02-17 10:54:38 +00:00
Harshil Patel
4d656c8f5f
Merge pull request #181 from drpatelh/fixes
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Fix tests for iVar variants
2021-02-17 10:08:57 +00:00
MaxUlysse
28fb5e8cbd
fix: update checksum or filename
2021-02-17 01:34:50 +01:00
Harshil Patel
412172cda6
Merge pull request #180 from MaxUlysse/master_tabix_bgzip
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Replace bcftools/bgzip by tabix/bgzip
2021-02-16 23:32:23 +00:00
drpatelh
c6a0976f52
Fix tests for iVar variants
2021-02-16 23:29:15 +00:00
MaxUlysse
596bb18394
fix: rename file to input and gz, plus fix tests
2021-02-17 00:28:32 +01:00
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
Harshil Patel
cf2f0762aa
Update main.nf
2021-02-16 23:06:26 +00:00
Harshil Patel
7c276d2974
Update tests/software/ivar/variants/main.nf
2021-02-16 23:01:27 +00:00
Harshil Patel
27020105aa
Update tests/software/ivar/variants/main.nf
2021-02-16 23:00:30 +00:00
Harshil Patel
de90d371dc
Update tests/software/ivar/variants/main.nf
2021-02-16 22:58:38 +00:00
Harshil Patel
23987bdad0
Update tests/software/ivar/variants/main.nf
2021-02-16 22:57:47 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix
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Replace bcftools/tabix by tabix/tabix
2021-02-16 22:30:45 +00:00
Harshil Patel
4f11064ae2
Update tests/software/tabix/bgzip/main.nf
2021-02-16 22:30:06 +00:00
Harshil Patel
8dd6d1d38a
Update tests/software/tabix/bgzip/main.nf
2021-02-16 22:29:13 +00:00
Harshil Patel
d6d34a4b5b
Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary
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Add gatk/createsequencedictionary
2021-02-16 22:21:38 +00:00
MaxUlysse
6a147b8aaa
chores: replace bcftools/bgzip by tabix/bgzip cf #179
2021-02-16 19:11:36 +01:00
MaxUlysse
5a144d6213
fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix
2021-02-16 18:35:32 +01:00
