Commit graph

11 commits

Author SHA1 Message Date
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)
* 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)
* 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)
* 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)
* 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)
* 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
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
Renamed from .github/filters.yml (Browse further)