612 commits

Author	SHA1	Message	Date
Paolo Cozzi	835ac48565	Fixing MULTIQC module and adding tests (#1) ... * fix multiqc process * fix multiqc tests * move multiqc test input data into tests/data/fastqc/ folder Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation * add multiqc github workflow * remove unused file * generalize multiqc input data User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report * update meta information	2020-12-01 12:03:37 +05:30
Abhinav Sharma	2783913122	initial attempt for multiqc module	2020-12-01 12:03:37 +05:30
drpatelh	e5c7ecc89c	Use STAR to build initial index for RSEM	2020-11-30 11:29:24 +00:00
Edmund Miller	6eeb930bdb	chore: Remove test directory from dummy tool	2020-11-24 21:09:55 -06:00
Edmund Miller	2fc39e02e2	test(trimgalore): Refactor se and pe to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	b2cd464ad3	test(samtools): Refactor stats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	36bbf6baa3	test(samtools): Refactor sort to use pytest-workflow ... Pretty sure this is passing it a sorted bam though?	2020-11-24 21:08:34 -06:00
Edmund Miller	6448638b55	test(samtools): Refactor index to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	16cb794892	test(samtools): Refactor idxstats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	34d86427a6	test(samtools): Refactor flagstat to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	7848019cdb	test(picard): Refactor markduplicates to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	939f5ca744	test(picard): Refactor collectmultiplemetrics to use pytest-workflow	2020-11-24 21:03:40 -06:00
Edmund Miller	234e85bdce	test(picard): Refactor mergesamfiles to use pytest-workflow	2020-11-24 19:01:12 -06:00
Edmund Miller	016d8684f3	test(bwa): Refactor to use pytest-workflow	2020-11-24 19:00:11 -06:00
Edmund Miller	ba681c6f27	refactor(pytest-workflow): Move fastqc tests to tests/	2020-11-24 20:26:04 +00:00
Edmund Miller	c264c66a49	test(fastqc): Use -entry to speed up tests ... `--wt, --workflow-threads` is now an option and can be used to run tests simultaneously.	2020-11-16 13:41:59 -06:00
Edmund Miller	a4544a11ad	chore(fastqc): Remove test output	2020-11-16 10:22:19 -06:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
drpatelh	47d390772c	Update picard version command and default container	2020-10-19 15:17:19 +01:00
drpatelh	29f9b05433	Update docs	2020-10-15 11:13:54 +01:00
drpatelh	530789ba85	Get tests passing	2020-10-15 10:47:15 +01:00
drpatelh	1d30e2c21a	Update tools not in rnaseq pipeline too	2020-10-14 18:59:25 +01:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
drpatelh	e9e81e8691	Revert RSeQC version	2020-10-12 17:47:13 +01:00
drpatelh	6bb3d5caea	Update container	2020-10-12 16:20:35 +01:00
drpatelh	64377d4035	Bug fixes	2020-10-12 16:20:22 +01:00
drpatelh	a1b705d412	Update RSeQC version	2020-10-12 16:04:04 +01:00
drpatelh	436a1f983c	Update trimgalore version	2020-10-12 15:59:46 +01:00
drpatelh	d19a8c702d	Update picard version	2020-10-12 15:58:09 +01:00
drpatelh	74f27803b4	Update stringtie version	2020-10-12 15:55:07 +01:00
drpatelh	f4f96ff792	Update gffread version	2020-10-12 15:52:05 +01:00
Harshil Patel	0e11679748	Update main.nf	2020-09-18 10:39:41 +01:00
Harshil Patel	fb44f36f66	Update main.nf	2020-09-16 19:08:24 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +01:00
drpatelh	cbf8329ffd	Add new modules	2020-09-10 16:09:54 +01:00
drpatelh	46edf8ae4c	Update featurecounts module	2020-09-10 16:07:21 +01:00
drpatelh	473f1b192f	Update functions script	2020-09-10 15:59:26 +01:00
Jeremy1805	789dc4f09a	Changed options.publish_files definition in functions.nf/initOptions	2020-08-20 11:57:10 +01:00
drpatelh	08723c9d61	Add tests for mergesamfiles	2020-08-07 16:39:16 +01:00
drpatelh	3547b64eab	Add docs and tests for markduplicates	2020-08-07 16:30:28 +01:00
drpatelh	cb85acddf0	Add docs and tests for collectmultiplemetrics	2020-08-07 16:29:37 +01:00
drpatelh	d6f7bb055b	Fix indents	2020-08-07 15:27:35 +01:00
drpatelh	e648dc335c	Add samtools stats commands	2020-08-07 15:23:39 +01:00
drpatelh	d5b16db27d	Add samtools sort	2020-08-07 15:21:28 +01:00
drpatelh	0287cad1f8	Add samtools index tests	2020-08-07 15:17:46 +01:00
drpatelh	17b5f5ef3b	Get samtools idxstats tests passing	2020-08-07 15:14:45 +01:00
drpatelh	46e4d35ec3	Get samtools flagstat passing	2020-08-07 15:12:03 +01:00
drpatelh	cf5cb8945c	Get samtools flagstat passing	2020-08-07 15:11:31 +01:00
drpatelh	736a0aa43c	Update indents and syntax	2020-08-07 15:05:25 +01:00
drpatelh	6333786d62	Add test BAM files	2020-08-07 14:04:39 +01:00
drpatelh	0ad26e3b19	Add output files	2020-08-07 13:28:18 +01:00
drpatelh	d10878f19d	Change to SE	2020-08-07 13:27:06 +01:00
drpatelh	7ab1245eb5	Add test data	2020-08-07 13:24:39 +01:00
drpatelh	b5338efb7d	Add tests for BWA mem	2020-08-07 13:24:24 +01:00
drpatelh	cff81ef875	Add test data	2020-08-07 12:57:32 +01:00
drpatelh	7604bd27fc	Add test nextflow.config	2020-08-07 12:56:52 +01:00
drpatelh	f367f9ef69	Add main test script	2020-08-07 12:56:39 +01:00
drpatelh	375af1428e	Minor change	2020-08-07 12:38:10 +01:00
drpatelh	a6fc702c8b	Update bwa index docs	2020-08-07 12:38:01 +01:00
drpatelh	36f2544c36	Add single_end input file for testing	2020-08-07 12:19:47 +01:00
drpatelh	6522b04ee3	Remove old code	2020-08-07 12:19:28 +01:00
drpatelh	30256d8e81	Update tests	2020-08-07 12:18:53 +01:00
drpatelh	2c0f552908	Add output files	2020-08-07 12:18:43 +01:00
drpatelh	4df72f0396	Update nextflow.config	2020-08-07 12:14:12 +01:00
drpatelh	f32950d0f2	Update docs for trimgalore	2020-08-07 12:10:42 +01:00
drpatelh	a63897ee9c	Add input output test folders	2020-08-07 11:40:51 +01:00
drpatelh	3a4fbf36ae	Add test	2020-08-07 11:31:07 +01:00
drpatelh	b1381bb577	Add TODOs	2020-08-07 11:30:55 +01:00
drpatelh	e657363900	Add nextflow config to folder	2020-08-07 10:59:05 +01:00
drpatelh	bdfe187440	Add TODO comments	2020-08-07 10:58:36 +01:00
drpatelh	9296897009	Define options as input	2020-08-07 10:58:24 +01:00
drpatelh	4f76bb6b03	Add nextflow.config	2020-08-07 10:06:45 +01:00
drpatelh	7efd46b489	Add nextflow.config	2020-08-07 09:59:19 +01:00
drpatelh	fab020461b	Add -with-docker	2020-08-07 09:44:16 +01:00
drpatelh	111b1505fa	Add basedir	2020-08-07 09:40:02 +01:00
drpatelh	75e7e1573c	Add output files	2020-08-07 09:32:28 +01:00
drpatelh	754fad7c8e	Update output paths	2020-08-07 09:32:03 +01:00
drpatelh	b0abd14135	Update tests	2020-08-07 09:31:27 +01:00
drpatelh	0466d5249b	Update docs	2020-08-07 00:50:49 +01:00
drpatelh	f014e67de6	Remove old outputs	2020-08-07 00:37:13 +01:00
drpatelh	2c7abca088	Move unit tests to deprecated	2020-08-07 00:36:05 +01:00
drpatelh	16d3ad5d06	Adapt script for meta	2020-08-07 00:35:34 +01:00
drpatelh	c98b32dfa8	Add link to functions file	2020-08-06 16:26:57 +01:00
drpatelh	e2b47a6fa3	Add software requirements section	2020-08-06 15:22:32 +01:00
drpatelh	2c9cd2d89b	Update main script	2020-08-06 12:00:38 +01:00
drpatelh	530b4c1bd9	Add test directory	2020-08-06 11:32:38 +01:00
drpatelh	b7d0ee043e	Initial commit	2020-08-06 11:32:18 +01:00
drpatelh	f021ab119b	Initial commit	2020-08-06 11:32:11 +01:00
drpatelh	ab512be9aa	Initial commit	2020-08-06 11:31:52 +01:00
drpatelh	f315a7b3c4	Hard copy files	2020-08-05 18:38:27 +01:00
drpatelh	ab8a9025a0	Copy across test data and docs for trimgalore	2020-08-05 17:28:25 +01:00
drpatelh	50fce8b3cf	Copy across test data and docs for samtools sort	2020-08-05 17:28:09 +01:00
drpatelh	de9d33da12	Copy across test data and docs for samtools index	2020-08-05 17:27:58 +01:00
drpatelh	fb697eca2f	Copy across test data and docs for bwa mem	2020-08-05 17:27:42 +01:00
drpatelh	da4dcee934	Copy across test data and docs for bwa index	2020-08-05 17:27:28 +01:00
drpatelh	5d224740cd	Change path	2020-08-05 17:17:58 +01:00
drpatelh	137db462a7	Add samtools	2020-08-05 17:17:47 +01:00
drpatelh	993d0d5743	Add picard	2020-08-05 17:17:41 +01:00
drpatelh	9d168cf29e	Add deeptools	2020-08-05 17:17:34 +01:00
drpatelh	f481899049	Add subread	2020-08-05 17:17:19 +01:00
drpatelh	20e6d847a3	Add trimgalore	2020-08-05 17:17:12 +01:00
drpatelh	c5bb9c2fde	Add macs2	2020-08-05 17:17:05 +01:00
drpatelh	f61ad7506a	Add homer	2020-08-05 17:16:56 +01:00
drpatelh	71d7aecf74	Add preseq	2020-08-05 17:16:45 +01:00
drpatelh	e94676a2b2	Add phantompeakqualtools	2020-08-05 17:16:34 +01:00
drpatelh	6fe4ec16df	Add ucsc	2020-08-05 17:16:23 +01:00
drpatelh	3b1669c317	Add bwa mem	2020-08-05 17:16:08 +01:00
drpatelh	7938a60a02	Add bwa index	2020-08-05 17:15:56 +01:00
drpatelh	7f5ca56413	Soft-link functions to top-level module dir	2020-08-05 17:03:04 +01:00
drpatelh	3ec4f63fd8	Use correct link to fastqc	2020-08-05 16:28:42 +01:00
drpatelh	c08e6959a5	Reorganise everything	2020-08-05 16:09:25 +01:00
Harshil Patel	95a91032ce	Merge pull request #42 from JoseEspinosa/bedtools_dev ... Add modules complement, genomecov, intersect, merge, sort for bedtools	2020-08-05 15:45:17 +01:00
Paolo Di Tommaso	70daf8be30	Minor style improvents ... This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses	2020-07-27 12:11:42 +02:00
Phil Ewels	3406ed4da0	Merge branch 'master' into fastqc-unit-test	2020-07-17 16:00:59 +02:00
Phil Ewels	f01b3f13a6	Remove debugging statement	2020-07-17 16:00:08 +02:00
Phil Ewels	2d1252c804	FastQC tests - disable hash check	2020-07-17 11:30:28 +02:00
Phil Ewels	dcc4beacb1	Fix FastQC test	2020-07-17 11:26:50 +02:00
JoseEspinosa	a09e3a633d	I forgot to uncomment output	2020-07-16 16:38:37 +02:00
JoseEspinosa	d30089f12d	Very preliminary implementation of passing optional params to bedtools/intersect modules	2020-07-16 16:37:33 +02:00
Stephen Kelly	846a862513	move md5 function to lib dir and symlink to fastqc test dir, rename md5 function	2020-07-16 09:17:48 -04:00
Phil Ewels	9dfafb4a19	Merge pull request #46 from stevekm/fastqc-unit-test ... add FastQC output validation and md5 checksum hash checks	2020-07-16 15:13:44 +02:00
Stephen Kelly	45fbbb538c	add FastQC output validation and md5 checksum hash checks	2020-07-16 08:20:37 -04:00
JoseEspinosa	759dd85c92	Removing biocontainer in favor of nf-core container	2020-07-16 10:22:09 +02:00
JoseEspinosa	6d8b616975	Bedtools sort adapted to the current module standard	2020-07-15 18:16:12 +02:00
JoseEspinosa	4d2e375a0d	Bedtools merge adapted to the current module standard	2020-07-15 18:16:01 +02:00
JoseEspinosa	98c8f44130	Bedtools intersect adapted to the current module standard	2020-07-15 18:15:49 +02:00
JoseEspinosa	0b123f9e13	Bedtools genomecov adapted to the current module standard	2020-07-15 18:15:32 +02:00
JoseEspinosa	2cbc988d5f	Bedtools complement adapted to the current module standard	2020-07-15 18:15:16 +02:00
FelixKrueger	e90164dd0b	Adding back tool specific input output and index files	2020-07-15 15:46:45 +01:00
drpatelh	532859d437	Update path	2020-07-15 14:07:19 +01:00
JoseEspinosa	7f8b8189f8	Merge remote-tracking branch 'upstream/master' into bedtools_dev	2020-07-15 15:05:26 +02:00
Gregor Sturm	a2bcb5c36a	Update module according to discussion on Slack	2020-07-15 13:04:49 +02:00
Gregor Sturm	01a926866e	Update software/fastqc/test/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:21 +02:00
Gregor Sturm	9d7cece077	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:11 +02:00
Gregor Sturm	5a8803ee2f	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:03 +02:00
Gregor Sturm	a3db769a93	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:52 +02:00
Gregor Sturm	180310bf0a	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:42 +02:00
Gregor Sturm	6ad2b570c2	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:30 +02:00
Gregor Sturm	53897f4d97	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:19 +02:00
Gregor Sturm	b00bb83532	Document params	2020-07-15 11:01:15 +02:00
Gregor Sturm	86d6daf9de	Implement publish_results parameter	2020-07-15 10:55:52 +02:00
Gregor Sturm	1dc47e7cd3	Make publishDir more flexible	2020-07-15 10:16:48 +02:00
Gregor Sturm	dd34fa5853	Use moduleDir for conda env	2020-07-15 09:48:17 +02:00
Gregor Sturm	f7c42ac4fd	Add tests for fastqc module	2020-07-15 09:48:14 +02:00
Gregor Sturm	167067a92e	Clean up module file	2020-07-15 09:47:41 +02:00
JoseEspinosa	c485d56972	Indentation error in yml	2020-07-14 18:00:23 +02:00
JoseEspinosa	562fc74550	Indentation error in yml	2020-07-14 17:57:42 +02:00
JoseEspinosa	39b9ca205c	Correcting path to test data	2020-07-14 17:42:03 +02:00
JoseEspinosa	b38135ff6b	Moving bedtools/intersectbed to bedtools/intersect	2020-07-14 17:40:17 +02:00
JoseEspinosa	c059a485b9	Using bedtools{_,-}genomecov instead of genomecov alone	2020-07-14 17:31:40 +02:00
JoseEspinosa	71eaa83bf6	bedtoools/complementBed changed to bedtools/complement	2020-07-14 17:26:45 +02:00
JoseEspinosa	8c3d7aa2d8	Standardizing process names to BEDTOOLS_FOO and same with some variables	2020-07-14 17:25:32 +02:00
JoseEspinosa	99a8196776	Module bedtools-sort added	2020-07-14 17:20:12 +02:00
JoseEspinosa	cf9d87c977	Module bedtools-merge added	2020-07-14 16:49:06 +02:00
JoseEspinosa	708cee9cae	Module bedtools-intersectbed added	2020-07-14 16:49:05 +02:00
JoseEspinosa	5f80a900e9	Changing fasta_sizes by chrom_sizes input path for genomecov	2020-07-14 16:47:27 +02:00
JoseEspinosa	f2eb3f68c0	Module bedtools-genomecov added	2020-07-14 16:47:26 +02:00
JoseEspinosa	f6894c7d3a	Module complementbed added	2020-07-14 15:50:35 +02:00
Phil Ewels	31c0f617b9	Fix up cutadapt tests	2020-07-11 17:14:14 +02:00
Phil Ewels	f36902b9af	Cutadapt - merge tests into one	2020-07-11 17:09:06 +02:00
Phil Ewels	d3f3432451	Update test file imports	2020-07-11 14:33:12 +02:00
Phil Ewels	014fef2e92	Rename tools to software	2020-07-11 14:27:21 +02:00