Commit graph

58 commits

Author SHA1 Message Date
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
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
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
14525ed50d Remove functions file 2020-10-14 18:29:50 +01:00
drpatelh
e438d026bd Unify syntax 2020-09-10 16:45:11 +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
736a0aa43c Update indents and syntax 2020-08-07 15:05:25 +01:00
drpatelh
375af1428e Minor change 2020-08-07 12:38:10 +01:00
drpatelh
2c0f552908 Add output files 2020-08-07 12:18:43 +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
f315a7b3c4 Hard copy files 2020-08-05 18:38:27 +01:00
drpatelh
5d224740cd Change path 2020-08-05 17:17:58 +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
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
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
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
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