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110 commits

Author SHA1 Message Date
kevinmenden
046444a736 added workflow files 2021-01-25 15:00:51 +01:00
kevinmenden
a1e1e27f67 updated test md5sums 2021-01-25 15:00:18 +01:00
kevinmenden
f58c1c1e9e added star genomegenerate test 2021-01-22 14:01:59 +01:00
Edmund Miller
daa25b9329
Merge branch 'preseq_test' 2021-01-15 17:41:13 -06:00
Edmund Miller
4f0c34bbfb ci: Bump nextflow version 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-15 10:32:20 -06:00
sruthipsuresh
7729fee5a9 Added gffread and gff3 file for testing 2021-01-15 10:32:20 -06:00
sruthipsuresh
b95bd37780 Added ucsc module 2021-01-15 10:28:11 -06:00
Harshil Patel
27dbe8b52a
Merge pull request #115 from Functional-Genomics-Lab/stringtie_test 
Added testing for Stringtie
 2021-01-15 16:09:39 +00:00
Edmund Miller
a3ca757f4e Update .github/workflows/phantompeakqualtools.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-15 09:38:13 -06:00
sruthipsuresh
3f814d1e2f Workflow and md5sums added 2021-01-15 09:38:13 -06:00
sruthipsuresh
2d2f15af0f
Delete phantompeakqualtools.yml 2021-01-13 21:23:24 -06:00
sruthipsuresh
b297f7aea1 Fixed test and removed phantompeak tests 2021-01-12 18:04:12 -06:00
sruthipsuresh
0a04c96357 Added module, TODO data 2021-01-12 09:13:37 -06:00
sruthipsuresh
cb39fcb915 Added preseq module and workflow 2021-01-12 08:41:09 -06:00
sruthipsuresh
522b896534 Workflow and md5sums added 2020-12-19 06:09:04 -06:00
Harshil Patel
c98f9284a2
Merge pull request #89 from KevinMenden/master 
Add bowtie module
 2020-12-18 14:56:29 +00:00
Edmund Miller
eb61638501
ci: Use verbose name for editorconfig-check 
I was getting confused myself with eclint
 2020-12-17 17:48:19 -06:00
Edmund Miller
c6cf653f25
ci(#77): Ignore README for editorconfig 
Because of the nf-core examples it throws errors.
 2020-12-17 17:48:02 -06:00
Edmund Miller
0b6f117d2a
ci(#77): eclint => editorconfig-checker 2020-12-17 17:48:02 -06:00
kevinmenden
8d3fc30eb3 fixed yml formatting 2020-12-17 07:39:34 +01:00
kevinmenden
d75cb75111 added singularity; edge NXF version 2020-12-17 07:33:44 +01:00
drpatelh
992232b340 Bump NF version to 20.11.0-edge 2020-12-14 00:14:28 +00:00
Edmund Miller
8d27ff53c5
ci: Support multiple nextflow versions 2020-12-09 09:56:40 -06:00
Edmund Miller
f994d55c18
style: Fix indent on workflows 2020-12-09 09:56:11 -06:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master 
Add multiqc module
 2020-12-09 11:31:07 +00:00
kevinmenden
fee0707af1 added bowtie_align workflow test 2020-12-08 14:19:34 +01:00
kevinmenden
73530e8df7 added bowtie index test github workflow 2020-12-08 14:13:30 +01:00
Abhinav Sharma
27b4b29976 Remove the extra data files 2020-12-04 20:20:59 +05:30
Edmund Miller
6d8ba714d5
ci(fastqc): Use 20.10.0 => '' 2020-12-04 08:23:19 -06:00
Abhinav Sharma
5fd3ba3ce6 Update the tests for MultiQC 2020-12-02 13:09:32 +05:30
Edmund Miller
65697532a1
ci: Get rid of software folder 2020-12-01 11:40:16 -06:00
Edmund Miller
8cd635f757
ci(fastqc): Fix test matrix 2020-12-01 11:13:43 -06:00
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
Edmund Miller
98c629583a
ci: Test whether subdirectories are breaking workflows 2020-11-30 19:03:56 -06:00
Edmund Miller
7d2b74a5f7
ci(fastqc): Use a test matrix for NXF versions 2020-11-30 18:57:56 -06:00
Edmund Miller
036427d73c
ci(pytest-workflow): Fix trigger paths 2020-11-24 21:24:55 -06:00
Edmund Miller
86219a586b
ci(trimgalore): Use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
445498d0c3
ci(samtools): Run tests with 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
ebf3a4529f
ci(picard): Update markduplicates 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
dfc8528df9
ci: Remove docker workflow 
This only applies to deprecated software
 2020-11-24 18:58:02 -06:00
Edmund Miller
691df9d469
style(actions): Create seperate software dir 
For future subworkflows
 2020-11-24 18:57:53 -06:00
Edmund Miller
f235732a58
ci(fastqc): Use both threads in GitHub runner 2020-11-16 13:45:00 -06:00
Edmund Miller
6d857a2584
ci(fastqc): Run pytest-workflow instead of workflow 
This will check for the actual output files and their contents not just
whether the module runs or not.
 2020-11-16 09:37:45 -06:00
drpatelh
082c582258 Remove EClint for now 2020-11-12 15:22:15 +00:00
drpatelh
b22ec332e9 Add GitHub Actions 2020-08-07 16:42:56 +01:00
drpatelh
50a628ad0a Remove deprecated tests 2020-08-07 15:55:23 +01:00