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Author SHA1 Message Date
James A. Fellows Yates
4f0b02b7b5
Typo fix 2021-09-20 13:00:11 +02:00
James A. Fellows Yates
3a0cd9d75a
Module docs transfer - point people to website! (#720) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Transfer module docs to nf-core website

* Missed a hyperlink

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update README.md

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-09-20 11:57:57 +01:00
kojix2
1c14be835b
Update the commands in the Using existing modules section (#698) 2021-09-09 09:32:33 +02:00
James A. Fellows Yates
6c633ef305
Specify in guidelines one should split CPUs when module has n > 1 tool (#660) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Describe CPU splitting

* Update README.md

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* More CPU examples

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
 2021-08-17 15:43:25 +02:00
James A. Fellows Yates
2a7c60e965
Guidelines update: describe workaround for modules called build (#647) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Update README.md
 2021-07-31 11:30:26 +02:00
James A. Fellows Yates
45dee96bdf
module: bwa/aln (#624) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* fix container paths

* Sync bwa version samese/sampe

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-27 08:13:48 +01:00
James A. Fellows Yates
f892f273fe
Updated optional input definition (#599) 
* Updated optional input definition

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 11:03:49 +01:00
Harshil Patel
e7e30b6da6
Bump Pangolin to 3.1.7 (#593) 
* Bump Pangolin to 3.1.7

* Update md5sum

* Update README

* Re-word

* Re-word again

* Use channels
 2021-07-20 12:25:36 +01:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567) 
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
 2021-07-07 10:10:18 +01:00
Charles Plessy
e84eaa22f3
Update pytest tag name for fastqc (#501) 
Running pytest with `--tag fastqc_single_end` does not work (it runs zero tests), as it appears that the tag name was changed to `fastqc` during the transition from underscores to slashes.
 2021-05-19 08:30:22 +01:00
Harshil Patel
6ade84b5cd
Update README.md 2021-05-04 11:25:30 +01:00
Edmund Miller
bdee7804ca
build: Bump version to 21.04.0 (#481) 
* build: Bump version to 21.04.0

Recent stable release https://github.com/nextflow-io/nextflow/releases/tag/v21.04.0

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-05-04 00:38:29 +01:00
Anthony Underwood
f9433639cf
Update README to include some git best practices (#415) 
* Update README to include some git best practices

* correct linting errors

* extra info about returning to master and deleting the branch

* use rebase

* stress importance of rebase

* Update README to include some git best practices

* correct linting errors

* extra info about returning to master and deleting the branch

* Changed position of git commands

* move later git commands down the action list
 2021-04-30 17:27:06 +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
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz (#395) 
* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
 2021-04-01 07:08:27 +02:00
Anthony Underwood
62775ea203
multi-tool instructions (#376) 
* multi-tool instructions

Add instructions on how to build a bespoke multi-tool Docker container and Singularity image

* fix linting issues

* Change bash to console

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-24 18:18:38 +00:00
Robert A. Petit III
6d14819859
Fix link describing process labels (#349) 2021-03-24 05:03:57 +00:00
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated (#336) 
* Add default output dir for modules that create indices

* Change path for index module test output

* Fix bowtie2/align tests

* Fixing bowtie/align tests

* Fix genomegenerate test

* Fixing README linting
 2021-03-23 17:55:01 +00:00
Harshil Patel
246011f59b
Add docs for running tests locally with pytest (#338) 
* Add docs for running tests locally with pytest

* Add docs for tag
 2021-03-23 15:29:52 +00:00
Maxime Garcia
e61f400167
feature: add new issue template for creating new module (#283) 
* feature: add new issue template for creating new module

* Apply suggestions from code review

* Apply suggestions from code review

Co-authored-by: Kevin Menden <kevin.menden@live.com>

Co-authored-by: Kevin Menden <kevin.menden@live.com>
 2021-03-19 15:39:22 +01:00
Harshil Patel
b85f331f82
Update docs in light of functionality being ported to nf-core modules subcommands (#281) 
* Add docs for existing modules

* Add new module checklist

* Update adding modules section

* Add links and spacing

* Adjust spacing

* Update pytest section

* Add create-test-yml docs

* Final updates

* Add minimum NF version

* Add some docs for Nextflow edge releases

* Indent bulleted section
 2021-03-19 12:06:54 +00:00
Gregor Sturm
94bdc62123 Only use one thread for pytest-workflow 
This avoids a race condition on the conda cache.
 2021-02-23 14:06:52 +01:00
Harshil Patel
678f104097
Update README.md 2021-02-09 13:27:30 +00:00
Edmund Miller
4c30f2943e
docs: Use one tag in all of the examples 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-08 20:13:11 -06:00
Edmund Miller
9637a8189a
docs: Update README with minor edits 2021-02-08 19:46:42 -06:00
drpatelh
c9cfdd31f3 Fix barfing linters 2021-02-08 00:57:06 +00:00
drpatelh
c92fe8701a Add docs about docs 2021-02-08 00:53:32 +00:00
drpatelh
41dfaf2a19 Use Nextflow comments 2021-02-08 00:44:45 +00:00
drpatelh
56752b90f5 Fix indents 2021-02-08 00:40:36 +00:00
drpatelh
a8efd112b9 Add docs about finding and adding containers 2021-02-08 00:35:50 +00:00
drpatelh
d4b278eb65 Update docs 2021-02-08 00:01:48 +00:00
drpatelh
9cb958ca25 Update commands for pytest 2021-02-07 23:50:21 +00:00
drpatelh
07f62a76c5 Re-word CI tests 2021-02-07 23:40:26 +00:00
drpatelh
6bbb71a022 Update link to tests template 2021-02-07 23:26:54 +00:00
drpatelh
83a50d8ae0 Rename SOFTWARE_TOOL to TOOL_SUBTOOL 2021-02-07 23:20:53 +00:00
Edmund Miller
e51d0bdf5e
Apply suggestions from code review 
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
 2021-02-05 09:26:45 -06:00
Edmund Miller
f065476d36
docs: Add testing documentation 2021-02-04 16:00:31 -06:00
drpatelh
e397c64c69 Add explicit Nextflow version to README 2020-12-14 00:08:38 +00:00
drpatelh
99f5d49d37 Update README 2020-10-20 11:04:12 +01:00
drpatelh
5eb735f561 Update README 2020-10-20 11:02:46 +01:00
drpatelh
7e2c7b1b41 Update README 2020-10-15 11:02:04 +01:00
drpatelh
d63982b41e Update README 2020-08-07 11:38:48 +01:00
drpatelh
fee1687215 Add template example to README 2020-08-07 11:30:43 +01:00
drpatelh
6255d9b00c Fix markdownlint 2020-08-07 10:10:12 +01:00
drpatelh
268c56c20d Update README 2020-08-07 09:31:54 +01:00
drpatelh
a0ca7b1738 Update meta.yml link 2020-08-06 16:30:32 +01:00
drpatelh
c98b32dfa8 Add link to functions file 2020-08-06 16:26:57 +01:00
drpatelh
70607cf5e2 Adjust spacing 2020-08-06 16:19:31 +01:00
drpatelh
b244160e78 Fix indent 2020-08-06 16:18:16 +01:00
drpatelh
bca0d598bf Add more links 2020-08-06 16:14:36 +01:00