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 )
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* 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 )
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* 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 )
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* 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 )
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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
3c4d9466f4
Adding minia for viralrecon ( #267 )
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* 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 )
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* 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
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
MaxUlysse
4968458b6c
chores: add cpus, memory and time requirements to limit resource consumption
2021-02-16 14:18:29 +01:00
drpatelh
fe3cb87f6d
Direct download Singularity containers
2021-02-03 20:03:45 -06:00
Edmund Miller
467d1595c4
test: Use docker image with singularity
2021-02-02 18:14:39 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order
2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:00:40 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
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The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
2021-02-02 12:44:30 -06:00
Edmund Miller
b96f2d6a5e
test(config): One config to rule them all
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 20:26:04 +00:00
