Commit graph

102 commits

Author SHA1 Message Date
Harshil Patel
20d8250d9f
Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
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