Commit graph

24 commits

Author SHA1 Message Date
Jose Espinosa-Carrasco
95e02f913f
Update comments with new style (#497)
* Update comment style on functions.nf files

* Update test main.nf comments

* Add meta for ggread
2021-05-12 14:56:46 +01:00
Kevin Menden
0b402ffda8
Move test data to nf-core/test-datasets (#432)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* move test data directory to nf-core/test-datasets

* bump multiqc version

* remove the test data

* updated test data link

* update README

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 12:32:39 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
Patrick Hüther
8a44258548
remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
drpatelh
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
drpatelh
c0926b0b6b various - add build to conda definition 2021-02-03 09:19:46 +00:00
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
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
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
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +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
FelixKrueger
e90164dd0b Adding back tool specific input output and index files 2020-07-15 15:46:45 +01:00
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