270 commits

Author	SHA1	Message	Date
JoseEspinosa	cee37852cd	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-02 09:15:20 +01:00
JoseEspinosa	579de3e038	bcftools_tabix generic for any TAB-delimited genome position file	2021-02-01 21:59:39 +01:00
drpatelh	f84e5b59ca	Rename bowtie_index to bowtie_build	2021-02-01 17:53:31 +00:00
Harshil Patel	0a41130276	Merge pull request #131 from KevinMenden/fastp-module ... Adding fastp module	2021-02-01 13:43:35 +00:00
Harshil Patel	e851da8640	Merge pull request #130 from KevinMenden/master ... Adding a QUAST module	2021-02-01 13:17:57 +00:00
Kevin Menden	f6c4e9d9c1	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:36 +01:00
Kevin Menden	9885da628e	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:22 +01:00
Kevin Menden	c807c6c438	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:15 +01:00
Kevin Menden	d88bf3bdda	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:06 +01:00
Kevin Menden	c43fe85a0c	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:02:57 +01:00
kevinmenden	038381de99	added fastp module	2021-02-01 13:54:08 +01:00
kevinmenden	b5298f94d8	refactored quast module	2021-02-01 13:13:21 +01:00
Harshil Patel	2c962f34df	Merge pull request #110 from luslab/master ... Add SEACR module containing a single CALLPEAK process	2021-02-01 09:48:15 +00:00
JoseEspinosa	0a8915ae77	Adding bcftools_tabix module	2021-02-01 10:07:35 +01:00
JoseEspinosa	52b0b8094d	Adding bcftools_stats module	2021-02-01 10:03:25 +01:00
JoseEspinosa	0423e686a6	Adding bcftools_isec module	2021-02-01 09:46:24 +01:00
JoseEspinosa	da7598272e	Adding bcftools_filter module	2021-02-01 09:41:08 +01:00
JoseEspinosa	eb12f4610d	Fixing meta ymls	2021-02-01 09:28:51 +01:00
kevinmenden	956bf22a58	fixed bug; updated meta.yml	2021-02-01 07:44:26 +01:00
JoseEspinosa	b6ef06c6cd	Add bcftools_consensus module	2021-01-31 22:23:26 +01:00
Harshil Patel	eadbea4b83	Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon ... Bowtie2 viralrecon	2021-01-30 13:22:30 +00:00
Harshil Patel	eab633776e	Update software/bowtie2/build/meta.yml	2021-01-30 13:21:56 +00:00
JoseEspinosa	500481833f	Adding bcftools_bgzip module	2021-01-30 11:22:25 +01:00
JoseEspinosa	986b72cee9	Fix error on previous commit	2021-01-30 09:35:25 +01:00
JoseEspinosa	29989035a5	Remove author entry from yml (copy-pasted :P)	2021-01-30 09:29:53 +01:00
JoseEspinosa	ddbe8055c2	Adding tests	2021-01-29 19:31:33 +01:00
JoseEspinosa	43f9815621	Adding module bowtie2 align	2021-01-29 19:29:32 +01:00
Harshil Patel	bd59706d51	Merge pull request #118 from heuermh/dsh-bio ... Added dsh-bio filter-bed as dsh_filterbed	2021-01-29 18:15:24 +00:00
Harshil Patel	7ab3217f16	Update software/dsh/filterbed/main.nf	2021-01-29 18:14:13 +00:00
Harshil Patel	cf5e38f48b	Update software/dsh/filterbed/main.nf	2021-01-29 18:14:08 +00:00
Harshil Patel	0fcbc4233c	Merge pull request #126 from JoseEspinosa/samtools_viralrecon ... Samtools viralrecon	2021-01-29 18:12:48 +00:00
Harshil Patel	eb7a3861db	Update software/samtools/mpileup/meta.yml	2021-01-29 18:12:17 +00:00
JoseEspinosa	2f9934c563	Adding bowtie2_build module	2021-01-29 18:57:27 +01:00
JoseEspinosa	13e9f81160	Fixing lint tests	2021-01-29 18:01:58 +01:00
JoseEspinosa	22dcdc692d	Adding samtools_mpileup module	2021-01-29 17:58:42 +01:00
JoseEspinosa	3eedca9bb4	Add samtools_view	2021-01-29 17:18:45 +01:00
kevinmenden	10bb80743a	started adding quast modules	2021-01-29 16:06:14 +01:00
Michael L Heuer	d2723408ad	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 09:01:21 -06:00
kevinmenden	d30994c6ef	Merge branch 'pangolin-module' of https://github.com/KevinMenden/modules into pangolin-module	2021-01-29 12:54:38 +01:00
kevinmenden	44df90a795	Merge branch 'master' of https://github.com/nf-core/modules into pangolin-module	2021-01-29 12:50:24 +01:00
Harshil Patel	5da41ecb26	Merge pull request #122 from KevinMenden/master ... Added tests and meta.yml files for Salmon	2021-01-29 11:49:03 +00:00
Harshil Patel	59e3e8202b	Update software/pangolin/main.nf	2021-01-29 11:43:42 +00:00
Kevin Menden	afaef3c30d	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 12:40:15 +01:00
kevinmenden	a22f430674	updated input description	2021-01-29 12:34:23 +01:00
Kevin Menden	8f2f936cd4	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 12:33:37 +01:00
kevinmenden	69a41cadbc	added pangolin module	2021-01-29 11:03:54 +01:00
kevinmenden	0780155dc4	added cutadapt module and tests	2021-01-29 09:33:45 +01:00
kevinmenden	3750bea2dd	fixed typo	2021-01-26 16:18:46 +01:00
kevinmenden	a3185732ff	added meta.yml files	2021-01-26 16:12:41 +01:00
kevinmenden	84355f674d	added optional output files	2021-01-26 13:31:30 +01:00