15 commits

Author	SHA1	Message	Date
Maxime Borry	aa76c6d870	new module: AdapterRemoval (#309) ... * 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) ... * 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) ... * 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) ... * 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) ... * 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)