ad426cb18c
new (fixed) module: entrezdirect/xtract ( #1926 )
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* first commit: module files
* last version main.nf
* modules/entrezdirect/xtract/meta.yml
* updated file
* updated test
* Update modules/entrezdirect/xtract/main.nf
changed name of output file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/xtract/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/entrezdirect/xtract/main.nf
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update tests/modules/entrezdirect/xtract/main.nf
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* updated test, removed esummary input file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2 years ago
f420d97ca2
renamed output in entrezdirect/esummary: xml ( #1928 )
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* renamed output: xml
* removed tail -n+3 from output
* removed comment
* removed blank space
* removed blank space
* updated test
2 years ago
7f7f6bc913
Add module `hamronization/abricate` ( #1925 )
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* Add hamronization/abricate
* Update input pattern in meta.yml
* Update location of hamronization test data
* Apply suggestions from code review
2 years ago
c363d8c37c
added gvcftools/extractvariants ( #1924 )
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* added gvcftools/extractvariants
* linting
* Update modules/gvcftools/extractvariants/meta.yml
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
* Update modules/gvcftools/extractvariants/main.nf
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
* added uncompressed input handling
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2 years ago
a8b0fce8ce
Tailfindr ( #1904 )
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* adding tailfindr module
* replacing the container
* removing todo
* removing todo and fixing meta.yml
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/tailfindr/test.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update main.nf
* Update meta.yml
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update meta.yml
* Update main.nf
* adding pytest
* Update main.nf
* Update modules/tailfindr/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update test.yml
* Update main.nf
* Update main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2 years ago
c9dc0a82d0
New Module: atlas/recal ( #1915 )
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* commit 08/07
* fixed formatting
* atlas recal commit - corrected formatting
* Fix tests
* Fix meta.yml
* Prettier
* Delete nextflow
* yaml > yml
* Delete meta.yaml
* Fix test
* Forgot to run prettier?
Co-authored-by: ltcrod <luca_traverso@kickseed.localdomain>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2 years ago
e5b44499ef
update multiqc and strelka modules version to have the same as the other modules using these ones ( #1914 )
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* update multiqc version in CUSTOM_DUMPSOFTWAREVERSIONS
* update stelka version in STRELKA_GERMLINE
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2 years ago
6b011dd148
SVDB MERGE samtools version ( #1913 )
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* Started (again) to work on bgzipping SVDB_MERGE output
* Updated test yml
* SVDB_MERGE now bgzips output
* Fixed singularity, renamed tests in test.yml
* Added samtools version
Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
2 years ago
839bc6b1ad
Amrfinderplus add tool and db version as output ( #1912 )
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* not yet working: add db version to versions.yml
* next try: db version number not in versions.yml
* Fix amrfinderplus versioning
* Update main.nf
* Apply suggestions from code review
* Update main.nf
* Dump version for syncrony with run
* Update test.yml
* Apply suggestions from code review
* add tool and db version to output
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update meta.yml
Co-authored-by: James Fellows Yates <jfy133@gmail.com>
2 years ago
8656636f0d
update for bcftools merge ( #1908 )
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* update for bcftools merge
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated test.yml
* added the bed file to the main input tuple
* merged all output into one output channel
* added a test for bcf.gz output
* Update modules/bcftools/merge/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* updated the tests
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2 years ago
8214b73700
SVDB_MERGE bgzip ( #1910 )
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* Started (again) to work on bgzipping SVDB_MERGE output
* Updated test yml
* SVDB_MERGE now bgzips output
* Fixed singularity, renamed tests in test.yml
Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
2 years ago
f91abed951
RGI/main export versions as explicit emission strings ( #1909 )
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* Export versions as explicit emission strings in addition to versions.yml for compatibility with hAMRonization
* Update YML
2 years ago
7e8ad56688
module FASTP: Support for interleaved FASTQ ( #1891 )
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* 1882 FASTP now supports interleaved FASTQ files
Changes:
- single_end FASTP pipes the FASTQ file
- Using args, it can be configured for interleaved in `--interleaved_in`
- Out is automatically interleaved if input is paired end.
- Removed md5sum checks for FASTQ files as compression seemed to cause
differences
- Instead, we check inside the FASTQ files for content.
Relates to #1882
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2 years ago
8d4373b4e8
added bcftools convert ( #1906 )
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* added bcftools convert
* Update modules/bcftools/convert/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* updated test.yml
* Update modules/bcftools/convert/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* added automatic output type detection
* linting
* removed a trailing whitespace
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2 years ago
6b9a6a5b29
bamsormadup: add extra test case, fix single file input ( #1905 )
2 years ago
8002e373b5
Amrfinderplus: add db-version to versions.yml ( #1899 )
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* not yet working: add db version to versions.yml
* next try: db version number not in versions.yml
* Fix amrfinderplus versioning
* Update main.nf
* Apply suggestions from code review
* Update main.nf
* Dump version for syncrony with run
* Update test.yml
* Apply suggestions from code review
Co-authored-by: James Fellows Yates <jfy133@gmail.com>
2 years ago
035e418369
Biobambam/bamsormadup: Fix name collision ( #1900 )
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* Fix name collision
Add stageAs to avoid name collisions
* fix version check
* fix test
2 years ago
720027275c
small update to samtools/merge ( #1896 )
2 years ago
ffe0375048
DRAFT: Extend output from snpeff ( #1895 )
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* Extending output from snpEff
* Test of additional output-files from snpEff
* Removing some md5 checks
2 years ago
535975eb81
Update bcftools/stats for WES ( #1893 )
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update bcftools/stats
2 years ago
6720d88f4e
Fgbio tmpdir modification ( #1890 )
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* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads
* Corrected fgbio call container, trying to fix fgbio group tests
* Removed incorrect line
* Changed tmp-dir to .
* Update modules/fgbio/groupreadsbyumi/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update modules/fgbio/fastqtobam/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Added callmol and sortbam
* fixed typo in callmol container
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2 years ago
1368164eb5
add module hamronization/amrfinderplus ( #1888 )
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* add module hamronization/amrfinderplus
* deleted comments
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2 years ago
9bda3dc7f0
Add new module: Pear ( #1779 )
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* create pear module
* add command and tests
* remove md5sum from known empty file
* add force -f to gzip and gunzip to avoid problems with symbolic links
* apply suggestions from review
2 years ago
edfe28a5e0
Variant recalibration ( #1885 )
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* update tests
* update
* update
* make the manta inputs consistant for germline/somatic/tumoronly
* match chromosomes to cram file (chr21)
* undo genotypegvfs
* undo genotypegvfs
* update VariantRecalibrator
* lint
* add '--resource:' tag
Co-authored-by: Smith Nicholas <smith@in.tum.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2 years ago
9deff5222e
Fixed the MD5 checksum ( #1881 )
2 years ago
3531824af8
Update DIAMOND module to output log file ( #1879 )
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* Update DIAMOND module to output log file
* Updating DIAMOND module to output log file - with jfy133 suggestions
Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2 years ago
013035eb5c
Improved kbtools/count ( #1884 )
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* Improved kbtools/count
* Update test.yml
removing TODO statements
* Update main.nf
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
2 years ago
c29b3fe11a
Updated container versions for fgbio ( #1878 )
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* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads
* Corrected fgbio call container, trying to fix fgbio group tests
* Removed incorrect line
2 years ago
9294259eea
Module/bcl2fastq ( #1883 )
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* add bcl2fastq
* test fixes
* fixed tests
* add tests to workflow
* change container source
2 years ago
f48a24770e
more generic name because of multiple extension ( #1880 )
2 years ago
1de4bd46b7
Add Merqury ( #1647 )
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* Add merqury files
* Remove md5sum for completeness stats file
* update container and test output
* Update modules/merqury/meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Explicitly set thread usage for meryl
* Remove empty file md5sum
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2 years ago
b4452a4881
Add ENTREZDIRECT/ESUMMARY ( #1833 )
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* first commit
* entrezdirect/esummary fixed version definition
* resolved suggestion
* updated main.nf
* changed output definition
* output: XML file
* output definition: XML file
* updated XML format in tests
* updated test file
* version: esummary instead of entrezdirect
* output file pattern: *.esummary.xml
* updated test file
* updated versions
* restored versions stdout
* updated test file
* changed xml_esummary pattern
* changed entrezdirect to esummary version
* updated test file
* Update modules/entrezdirect/esummary/meta.yml
changed output file pattern: "*.xml"
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/meta.yml
updated keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Output file pattern: *.xml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Output file pattern: *.xml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
database as separate input channel
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* removed blank spaces in input definition
* database as separate channel
* conditional script for stdin
* updated input definition
* entrez-direct version:16.2_1
* all input channels are separate
* ignore stderr, catch xml stdout
* removed blank lines
* added ids file input
* updated test
* conditional script for input
* removed bad definition of input file
* updated test file
* Update modules/entrezdirect/esummary/main.nf
changed input definition: ui, uids_file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/meta.yml
added uids_file description
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esummary/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* input: uid or uids_file
* updated input
* added uids_file to input
* input file as optional input
* input file as optional input in each test
* new conditional script
* unpdated test file
* single input definition
* added error messages
* updated test
* removed cat from command output
* Update modules/entrezdirect/esummary/main.nf
added comment on use of grep in output
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added comment
* removed blank spaces
* input file: empty list
* input file: empty list
* removed comment at wrong position
* optional file defined as empty list
* updated successful test
* Apply suggestions from code review
Accepted suggestions.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update modules/entrezdirect/esummary/main.nf
Fixed comment.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update modules/entrezdirect/esummary/main.nf
Updated grep in output file.
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* added tail -n+3 before output
* updated successful test
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2 years ago
d8bef6057b
update snpeff to 5.1 and cache up to 105 ( #1877 )
...
* update snpeff to 5.1 and cache up to 105
* update dm5checksum
2 years ago
973151e9ea
update ensemblvep to 106.1 and cache to 106 ( #1876 )
2 years ago
b6ed584443
Update MOTUS/PROFILE module to output log file ( #1871 )
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* Add saving of stderr output as a log file as it contains summary statistics
* Apply suggestions from code review
2 years ago
957cb9b836
Update filtlong module to output log file ( #1873 )
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Redirect logging information to log file in filtlong module
2 years ago
b78e19b9da
Update PORECHOP module to output log file ( #1870 )
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Update porechop to output log file
2 years ago
ec806cebf1
diminish memory demand ( #1872 )
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* diminish memory demand
Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.
So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.
* fix prettier
* removing TODOs
2 years ago
589f39c39e
Add manual version definition for artic modules ( #1867 )
2 years ago
49366ef275
Add CITATION.cff file for the nf-core publication ( #1865 )
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* Add CITATION.cff file for nf-core publication
* Update .editorconfig .cff files
2 years ago
b2a8464e3e
This updates the fgbio container version ( #1863 )
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* This updates the fgbio container version
* Also updated conda install command
2 years ago
b5facb2db2
Ataqv mkarv ( #1857 )
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* first draft
* fix test run
* Apply suggestions from code review
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/ataqv/mkarv/test.yml
* Update tests/modules/ataqv/mkarv/test.yml
* Update tests/modules/ataqv/mkarv/test.yml
* Update tests/modules/ataqv/mkarv/test.yml
* Update tests/modules/ataqv/mkarv/test.yml
* Update modules/ataqv/mkarv/nextflow.config
* Delete nextflow.config
* Update tests/modules/ataqv/mkarv/test.yml
* fix linting
* fix linting
Co-authored-by: bjlang <>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2 years ago
0825fff505
Bump ataqv version ( #1860 )
...
* Bump ataqv version
* Remove check for empty file
2 years ago
682f789f93
Bump tool versions for modules required in viralrecon ( #1859 )
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* Bump tool versions for modules required in viralrecon
* Fix all the tests
* Fix Prettier lint
* Remove empty md5sums
2 years ago
2f1eca7467
Adjust requested ressources for `gstama/merge`, `isoseq3/refine`, `lima`, `ultra/align` ( #1858 )
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Reduce requested resources
2 years ago
b02e648c22
Add MOTUS/MERGE ( #1734 )
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* Add motus/merge module, missing test yml
* Fix prefix
* Fix polymersase
* Update test meta.yml
* Try new version system
* Typo fix
* Clairfy docs for the version file
* Switch to directory auto detection
* Now with the change and not just meta
* Remove now unneeded input parameter from test
* Fix input type check
* Try adding db requirement to fix docker issue
* Update modules/motus/merge/main.nf
* Fix input
* Apply suggestions from code review
* Fix md5sums
* Replace debugging db location with actual
* Fix contains due to further varialbility
* Indenting
2 years ago
43d05d5482
fix (1852): picard/collectmultiplemetrics supports CRAM ( #1853 )
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* fix (1852): picard/collectmultiplemetrics supports CRAM
Changes:
- Add .fai input to Picard CollectMultipleMetrics
- Now supports CRAM effectively.
- Will break existing pipelines!
Fixes #1852
* 1852 Update meta.yml to include .fai
2 years ago
848ee9a215
Improve descriptions for modules with missing
...
Description and keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2 years ago
5138acca09
Fix MultiQC conda ( #1856 )
2 years ago
16536b6936
removed extra ) in the version strings ( #1850 )
2 years ago
Alexander Ramos Díaz