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Author SHA1 Message Date
drpatelh
e397c64c69 Add explicit Nextflow version to README 2020-12-14 00:08:38 +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
Harshil Patel
5561fb58d8
Merge pull request #90 from nf-core/ci-nextflow-matrix 
Support multiple nextflow versions in CI
 2020-12-10 12:39:00 +00:00
Harshil Patel
deb0a103db
Merge pull request #92 from drpatelh/salmon 
Update Salmon modules
 2020-12-09 23:01:06 +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
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
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
Abhinav Sharma
5949bfc15b Edit the location of multiqc_config file 2020-12-04 22:55:15 +05:30
Abhinav Sharma
27b4b29976 Remove the extra data files 2020-12-04 20:20:59 +05:30
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
Edmund Miller
6d8ba714d5
ci(fastqc): Use 20.10.0 => '' 2020-12-04 08:23:19 -06:00
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
84c0bda00e Apply suggestions from code review by @Emiller88 2020-12-03 12:57:24 +05:30
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
6404c3390d
ci(fastqc): Remove md5sums 
These may not work across nextflow versions
 2020-12-01 11:18:55 -06:00
Edmund Miller
8cd635f757
ci(fastqc): Fix test matrix 2020-12-01 11:13:43 -06:00
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
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
Harshil Patel
e02f0de514
Merge pull request #87 from drpatelh/rsem_index 
Use STAR to build initial index for RSEM
 2020-11-30 14:45:32 +00:00
drpatelh
e5c7ecc89c Use STAR to build initial index for RSEM 2020-11-30 11:29:24 +00:00
Edmund Miller
036427d73c
ci(pytest-workflow): Fix trigger paths 2020-11-24 21:24:55 -06:00
Edmund Miller
6eeb930bdb
chore: Remove test directory from dummy tool 2020-11-24 21:09:55 -06:00
Edmund Miller
86219a586b
ci(trimgalore): Use pytest-workflow 2020-11-24 21:08:34 -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
445498d0c3
ci(samtools): Run tests with 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
ebf3a4529f
ci(picard): Update markduplicates 2020-11-24 21:08:33 -06:00
Edmund Miller
d1a77b2fb2
test(picard): Add failing test for markduplicates 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
d009420a0c
test(fastqc): Fix md5sums 
These must have gotten messed up at some point
83539fcdf2 is my guess
 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