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237 commits

Author SHA1 Message Date
Harshil Patel
b236d0c834
Update main.nf 2020-12-17 10:24:01 +00:00
kevinmenden
57ab6dbcbf groovy formatting 2020-12-17 10:24:48 +01:00
kevinmenden
d75cb75111 added singularity; edge NXF version 2020-12-17 07:33:44 +01:00
kevinmenden
f35850bf14 bowtie bam output 2020-12-16 11:02:58 +01:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
99a2364a26 Update all other modules 2020-12-14 00:05:48 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
drpatelh
115efec15c Update Salmon quant to use BAM input 2020-12-09 21:20:52 +00:00
drpatelh
37b8b82c98 Fix tyop 2020-12-09 21:20:26 +00:00
drpatelh
42f318fe75 Update Salmon modules 2020-12-09 21:20:11 +00:00
kevinmenden
42020ce5ac added tests for bowtie paired-end alignment; resolved index bug 2020-12-09 16:39:05 +01:00
kevinmenden
cc72028d3d output index as directory 2020-12-09 15:58:56 +01:00
Kevin Menden
560a6a578b
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-09 15:45:05 +01:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master 
Add multiqc module
 2020-12-09 11:31:07 +00:00
Abhinav Sharma
0c9f29e0a2 Give finishing touches after the review 2020-12-08 19:08:00 +05:30
Abhinav Sharma
b56a0322ab
Apply suggestions from code review by @drpatelh 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-08 18:57:14 +05:30
kevinmenden
9d67da2b2c added module yml files 2020-12-08 13:40:32 +01:00
kevinmenden
508761e05c Added bowtie index and align modules 2020-12-08 12:57:00 +01:00
Harshil Patel
cd2cf9cf2f
Merge pull request #85 from nf-core/pytest-workflow-refactor 
Refactor all tests to use pytest-workflow
 2020-12-04 14:30:00 +00:00
Abhinav Sharma
3da7aec183 Update the signatures 2020-12-04 12:25:16 +05:30
Abhinav Sharma
a30df8a59b Iterate again on MultiQC 2020-12-04 12:11:17 +05:30
Abhinav Sharma
5fd3ba3ce6 Update the tests for MultiQC 2020-12-02 13:09:32 +05:30
Abhinav Sharma
4e657c82e2 Move the MultiQC test files to data folder 2020-12-01 12:27:31 +05:30
Abhinav Sharma
b43c1f3937 Refactor the multiqc test code 2020-12-01 12:19:52 +05:30
Abhinav Sharma
131609dc05 Tweak the output section to make the tests pass 2020-12-01 12:03:37 +05:30
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