Commit graph

537 commits

Author SHA1 Message Date
Harshil Patel
b6e4ecabba
Add Nextclade module (#484)
* Bump pangolin version

* Add nextclade to software list

* Add nextclade module

* Update md5sum for Pangolin due to version bump

* Adding some URL to meta.yml

* Adding new line at end of file

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-05-06 15:48:15 +01:00
Yuk Kei Wan
faf77d6fee
add nanolyse module (from nanoseq modules) (#471)
* add nanolyse modules

* add clean.fastq.gz path and md5sum

* fix errors

* remove unreproducible md5sum

* solve linting problem

* address PR suggestions

* GET_NANOLYSE_FASTA as a local module

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/meta.yml

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

* Update software/nanolyse/meta.yml

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

* Update tests/software/nanolyse/test.yml

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

* Update tests/software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* update to the version from nf-core/tools-dev

* input and output files cannot have the same names

* Update test.yml

* Update software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* Update test.yml

* revert

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-05 11:20:09 +01:00
Michael L Heuer
e3cf4c822c
Update dsh-bio modules to version 2.0.4 (#482)
* Update dsh-bio modules to version 2.0.4

* update docker tag

* update md5 checksums

* Update software/dshbio/filtergff3/main.nf

* Update software/dshbio/splitgff3/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 14:28:44 +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
Kevin Menden
5e86245388
updated paths to test data (#478)
* updated paths to test data

* Update test_data.config

changed file names
2021-05-03 07:13:07 +01:00
Yuk Kei Wan
6ad50f8ec4
Add stringtie merge module (from nanoseq modules) (#475)
* add stringtie merge module

* add md5sum and path for stringtie.merged.gtf

* fix errors

* try fixing stringtie check error

* add tag

* remove unreproducible md5sum

* address PR suggestions

* hopefully fix linting error
2021-05-03 07:18:51 +02:00
Charles Plessy
16d20a7cc4
New last/lastdb module to index sequences before alignment. (#476)
* New last/lastdb module to index sequences before alignment.

The `lastdb` command creates a sequence index for the LAST aligner
(https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ
format, and compression is handled automagically.  DNA or protein
sequences can be indexed.

The sequence index is a collection of files sharing the same basename.
This module sets the basename to the sample identifier (`$meta.id`) and
creates the index in a directory always called `lastdb`.  The module's
output channel then conveys a copy of the metadata and the path to the
`lastdb` directory.

Other modules will follow (see Issue #464).  The LAST aligner can align
proteins to proteins, DNA to DNA and can translate DNA align to
proteins.

* Remove trailing whitespace.

* Apply suggestions from code review

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

* Update as suggested in PR.

* Attempt to pass linting.

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 11:36:31 +01:00
Harshil Patel
466ab67808
Fixes for nanoseq modules (#479)
* Fix minimap2 index module

* Fix minimap2 index tests

* Fix graphmap2 index module

* Fix graphmap2 module

* Fix ECLint

* Fix bedtools bamtobed module

* Fix tests for bedtools bamtobed module

* Add tag for graphmap2 align module

* Fix EClint

* Fix qcat module

* Add md5sum for graphmap2/align module

* Remove non-started test data file

* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00
Yuk Kei Wan
05f479f03a
add qcat module (from nanoseq modules) (#469)
* add qcat module

* remove md5sum(nom-reproducible)
2021-04-30 13:20:56 +01:00
Yuk Kei Wan
3f804ee667
add bedtools bamtobed module (from nanoseq modules) (#466)
* add bedtools bamtobed module

* fix erros

* fix linting problem
2021-04-30 13:20:31 +01:00
Yuk Kei Wan
a8720463ac
add graphmap index and align modules (from nanoseq modules) (#468)
* add graphmap index module

* add graphmap2/index

* add graohmap2 align module

* remove graphmap2 align md5sum
2021-04-30 13:18:58 +01:00
Yuk Kei Wan
05b067e907
add minimap2 index module (#467) 2021-04-30 13:18:11 +01:00
Kevin Menden
bbf8626b28
Bugfix (#477)
* 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

* remove the test data again

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-30 07:32:10 +02:00
Florian Wuennemann
88dda738ac
Added kallistobustools/count (#409)
* Basic kb-python count functionality for scRNA-seq quantification working.

* Added tests and test data for workflow kite.

* Removed trailing whitespace

* Changed output channels to tuples with meta

Based on suggestions by @KevinMenden.

* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.

* Update software/kallistobustools/count/main.nf

@KevinMenden fixed wrong path definition

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

* Increased version of kb-python

* Updated tests with raw links.

* Fixed subtool referencing: kallistobustools/count

* Added newline

* Update software/kallistobustools/count/main.nf

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-04-30 07:27:17 +02:00
Anthony Underwood
6a31737cb8
Raxmlng (#474)
* raxml-ng is compute intensive - upgrade process label to high

* ensure raxmlng uses --all when bootstrapping

* remove block that should be taken of by the options passed in

* update tests
2021-04-29 08:20:05 +01:00
FriederikeHanssen
9ce4427275
Add gvcf index files (#472) 2021-04-28 20:23:10 +01:00
Florian Wuennemann
a5d0cf3686
Update kallistobustools/ref module (#465)
* Bump version and format references to use raw params.test_data

* Apply suggestions from code review

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

* Updated tags

Missed on in last commit.

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-04-28 14:54:40 +02:00
Daniel Lundin
d7a3286a9a
New module to use hmmalign from HMMER to align sequences (#470)
* Ignore vim tmp files

* Added hmmalign module, not yet tests

* Test output

* Replaced functions.nf for hmmalign with upstream

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/meta.yml

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/test.yml

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

* Update tests/config/pytest_software.yml

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

* Update software/hmmer/hmmalign/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-28 11:21:24 +01:00
Jose Espinosa-Carrasco
d63ff4ba1b
Add artic guppyplex (#455)
* Adding artic guppyplex module

* Adding guppyplex tests

* Fix tests

* Correcting typo

* Fix lint

* Fix test

* Missing description

* Missing descriptions

* Update functions to last version as suggested

* Bump newest version of nanoplot
2021-04-27 15:57:34 +01:00
Harshil Patel
9ea7f50963
Bump plasmidid version (#460)
* Bump plasmidid version

* Fix tests
2021-04-26 12:40:38 +02:00
FriederikeHanssen
ae154b8c3f
Add human data paths (#458)
* Add new human data and fix sarscov paths

* Fix filename typo

* Apply code review

* replace index with to match sarscov data

* lower case

* indent everythin

* Adapt sarscov keys to new naming convention

* Update test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 15:30:43 +01:00
Kevin Menden
f7e3b8260c
change process.time for tests to 2h (#452) 2021-04-16 13:08:03 +01:00
Harshil Patel
d1c6082a66
Update modules required for rnaseq pipeline (#449)
* Update HISAT2 build module

* Bump preseq version

* Fix tests

* Add meta.yml for preseq to fix linting

* Auto-detect --genomeSAindexNbases for smaller genomes

* Add placeholder to use human data for the tests

* Add CSI output option to samtools/index

* Fix samtools/index tests
2021-04-16 08:56:47 +01:00
Harshil Patel
defaca4f1b
Add ucsc/bedclip module (#450)
* Add ucsc/bedclip module

* Fix tests

* Fix nf-core lint
2021-04-15 22:04:59 +02:00
Anthony Underwood
2ed9b6ae28
Raxmlng (#443)
* new raxml module

* new raxml module

* pass in args for bootstrap and add test for support file

* remove unnecessary tag

* ensure tags meet guidleines

* Apply suggestions from code review

* Update to latest functions file

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 08:38:59 +01:00
Jose Espinosa-Carrasco
750bd8c3e3
Finish deeptools modules (#442)
* Adding bigWig and deeptools computeMatrix files to config

* Adding meta.yml for deeptools modules

* Add test for deeptools modules

* Fixing and reordering tags

* Fixing conda test that worked in local...

* Apply suggestions from code review

* Changing bigwig file pattern to include bigwig extension

* Saving after last change is a good practice

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 21:48:43 +01:00
Kevin Menden
043a7d1e3c
remove deprecated test tags (#440)
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
2021-04-13 18:03:09 +01:00
Jose Espinosa-Carrasco
a9fcbd93cc
Move assembly test files from genome to illumina (#441)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes

* Update test path in config for illumina assembly files

* Update modules using assembly files

* Correctly setting path of assembly files

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 12:52:11 +02:00
Jose Espinosa-Carrasco
26fdebc8de
FIx plasmidid tests for new contigs.fasta file (#438)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes
2021-04-13 08:49:44 +01:00
Kevin Menden
1d874bb0d0
Finish rseqc modules (#439)
* 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

* added rseqc/bamstat tests

* added tests/meta.yml for rseqc/inferexperiment

* added test/meta.yml for rseqc/inner_distances

* added meta.yml and tests/main.nf for junctionannotation (test not running)

* added test/meta.yml for rseqc/readdistribution

* finished test/meta.yml for rseqc/readduplication

* added entries to pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 08:49:32 +01:00
Thanh Lee
c736817598
🧸 Updated rasusa (#437)
* changed genome size input position

* fixed...😊
2021-04-12 21:47:55 +01:00
Harshil Patel
c99ab09f8d
Add kraken2 pigz multi-tool container for compressing output fastq files (#434)
* Add kraken2 pigz multi-tool container for compressing output fastq files

* Add untar to pytest config

* Add untar process to kraken2 tests

* Remove unneeded tags
2021-04-12 18:47:34 +02:00
Anthony Underwood
df8910de4e
Iqtree (#435)
* Resolve suggests after PR review

* add newline to functions

* need variable interpolation using double quotes; remove unnecessary tag

* add a more resilient link to raw github files

* remove trailing slash

* Update software/iqtree/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 17:01:26 +01:00
Jose Espinosa-Carrasco
3ac21ff0dc
Add abacas module (#431)
* Add abacas module

* Add test for abacas module

* Add Harshil to authorship

* Updating test with the data uploaded to nf-core/datasets

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 15:37:08 +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
Jose Espinosa-Carrasco
2c43c39ccc
Add pycoqc module (#424)
* Add pycoqc module

* Adding pycoqc module tests

* Update pycoqc wilth new functions.nf

* Update tests to check for json report content
2021-04-12 10:52:14 +01:00
Anthony Underwood
575df10781
add new iqtree module (#427)
* add new iqtree module

* Resolve suggests after PR review

* add newline to functions
2021-04-12 09:45:56 +01:00
Thanh Lee
ec15bae344
🏋️‍♀️ new submodule mash/sketch🕺 (#426)
* new submodule mash/sketch

* fixed submodule naming

* OK, tag is diff to keyword

* OK  another round 🤣

* removed TODO comments

* updated as per review comments 🙆‍♂️

* updated functions.nf 😁

* Update software/mash/sketch/main.nf

* Update main.nf

Removed blank line at the 12th

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 16:24:23 +01:00
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420)
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
Thanh Lee
5a59e61052
new module: rasusa (#413)
* new module: rasusa

* Removed blank line in software/rasusa/main

* updated code as per reviewcomments

* removed blank line as failed for lint

* updated as per review comments

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:10:32 +01:00
Anthony Underwood
ca776e76a2
add rapidnj module (#421)
* add rapidnj module

* remove trailing whitespace

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:04:54 +01:00
Florian Wuennemann
0f53c3b96b
Added kallistobustools/ref (#408)
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me

* Removed trailing whitespace line 29

* Moved workflow from meta to options.

* Update main.nf

* Forgot to remove previous testing input channel for workflow.

* Apply suggestions from code review

Applied changes suggested by @drpatelh

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

* Added gtf to meta.yml.

* Apply suggestions from code review

Adding @drpatelh suggested changes.

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

* Moved workflow to input value. Fixed tests.

* Update tests/software/kallistobustools/ref/test.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 09:41:41 +01:00
Yuk Kei Wan
16e8d21477
Nanoplot and sequencing_summary.txt for Nanopore test data (#364)
* add nanoplot

* add Nanopore 100 read subset bam and fastq

* add nanoplot module and sequencing_summary.txt

* Update pytest_software.yml

* Update main.nf

* test directory path

* testing one output file

* Update main.nf

* fix typo

* remove path to test outputs (it worked locally)

* use test_data.config in test

* add meta.yml

* allowing either summary.txt or fastq.gz inputs

* fix linting and test.yml

* test whether github check can catch the output

* add summary.txt test output paths

* check Nanoplot-report.html output
2021-04-09 08:31:38 +01:00
Anthony Underwood
6927f1d086
New Snpsites module (#416)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* revert to gubbins test on upstream

* add new lines

* renove whitespace

* Apply suggestions from code review

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 08:00:33 +01:00
Anthony Underwood
63b3975292
Update gubbins module to use new files (#417)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* remove snpsites from gubbins branch

* remove redundant test_fas alignment

* update md5 sums

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco
f90dde0d88
Add plasmidid module (#410)
* Adding plasmidid module

* Adding test for plasmidid module

* Update plasmidid version to 1.6.4

* Adding contigs.fasta file

* Update tests

* Adding output files on test.yml
2021-04-08 22:44:30 +01:00
Anthony Underwood
be390a25e5
adding fasttree module (#412)
* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* remove TODO

* update test data naming

* further test data naming updates

* remove options in favour of $options.args

* ensure non standard exit codes don't cause an issue

* update md5sum
2021-04-08 18:15:23 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389)
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
avantonder
710ab76b90
new module: gubbins (#377)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-07 16:31:24 +01:00
Harshil Patel
242fdb2f73
Version bumps and minor module updates (#406)
* Version bumps and minor module updates

* Fix Pangolin tests

* Fix SPAdes tests

* stageAs @phue
2021-04-06 13:38:41 +01:00
Patrick Hüther
3b1dcc9cc0
MethylDackel: fix version scraping (#401)
* methyldackel: fix version scraping

* fix output file path
2021-04-06 10:59:33 +01:00
Jose Espinosa-Carrasco
f8e428d690
Restructuring spades tests whith new test data sets + fixing spades tests (#396)
* Restructuring with new test data sets + fixing tests

* Remove checkings for warning files

* Remove md5 check for test.gene_clusters.fa

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:31:23 +01:00
Robert A. Petit III
c9256616b9
update tests for new config (#384)
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:22:06 +01:00
Nicholas Toda
f126d980d7
Add tests for subread #106 (#393)
* inital commit

* added meta.yaml info

* add initial logic for featurecounts test

* add args and change SE/PE to strandedness for featurecounts test

* added tests to pytest

* added test.yml

* removed GTF flag in options

* corrected test meta params

* meta yaml corrected tool info

* update test.yml

* fix lint errors meta.yml

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
2021-04-01 20:02:36 +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
sruthipsuresh
983ba000c1
New modules: Fgbio callmolecularconsensusreads and sortbam (#352)
* Added fgbio callmolecularconsensusreads and sortbam modules

* Fixed naming issue in meta.yml

* fix: test.yml and config lint

* Revert "fix: test.yml and config lint"

This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail.

* style: Fix test names

* style: Remove trailing whitespace

* fixed test.yml

* fix: test data in sortbam

* fix: data format

* fix: test data for callmolecularconsensusreads

* Corrected with updated test data

* Apply suggestions from code review

Applied changes from code review, mainly syntactical changes

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

Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 20:38:50 +01:00
JJ
e50a525715
gatk4 markduplicates (#356)
* new module gatk4/markduplicates

* add tests

* add gatk4_markduplicates entry in pytest_software.yml

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Apply suggestions from code review

* Fix EC lint

* Update md5sum

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update tests/software/gatk4/haplotypecaller/main.nf

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

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00
Nicholas Toda
e526eae472
Add tests for hisat2 (#366)
* initial commit hisat2/build

* initial commit hisat2/build

* changed names for hisat2

* fixed directory structure and args

* added splice site test data

* added splice site inputs

* replaced list with individual args

* fixed removed commas

* added test yml file

* updated hisat2 conda version

* added meta.yml

* added meta.yml description

* added meta.yml inputs

* added meta.yml outputs

* update conda version for hisat2

* removed trailing whitespace meta.yml

* fixed version number for containers

* added test data to test config

* updated for new test logic

* fix pytest issue?

* fix pytest issue

* fixed wrong tool in meta.yaml

* updated tets.yaml name

* handle build bug for testing

* handle build bug for testing in yaml

* moved test folder to fix build bug

* use old hisat2 version to avoid conda giving inconsistent md5sum

* initial commit

* removed temp file

* added meta yaml

* add to pytest

* added tests

* added test yml

* add align meta yaml

* add hisat2 align to pytest

* remove need for splice data by calling process

* add hisat2 align se test

* add hisat2 align pe test

* update names hisat2 align

* update software pytest for using mutiple modules

* remove splice site test data since using module instead

* remove splice site from config since using module instead

* fixed extra brace

* added hisat2 align test.yml

* removed md5sum for bam files

* updated build md5sums

* Apply suggestions from code review

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
kevbrick
fead37d57a
Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)
* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Fix 4-spacing issues (caught in PR linting)

* Code review fixes & update configs

* Code review: remove stray echo

* Code review: Add msisensor modules

* Slashes to underscores to get tests to run on github

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Add all outputs to meta.ymls

* Fixes from code review

* Fixes from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 16:46:00 -04:00
Batool
f90b8ecb24
Fix the test path salmon/index and quant after switching to config data (#385)
* fix the test path in main.nf for salmon/index and quant

* fix typo

* Apply suggestions from code review

* Apply suggestions from code review

* Apply suggestions from code review

Mannnn, hopefully I finally got it right :)

* replaced /salmon/salmon/ with /index/salmon/

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 17:03:25 +00:00
FriederikeHanssen
555f1710e0
Update test paths in bwa mappers (#387)
* Update test paths in bwa mappers

* Fix indentation

* indices pass lcoally now

* no idea how they could ever pass before, Tests pass locally no

* Update samtools and bwamem2 versions

* Correct mulled containers + md5
2021-03-25 09:24:21 +00:00
Kevin Menden
6973df628f
Fixing vcftools and bismark tests (#383)
* fixed vcftools

* fixed genomepreparation, methylationextractor

* fixed deduplicate
2021-03-25 09:12:08 +00:00
Jose Espinosa-Carrasco
13bd67ed8a
Fix some module test after adapting test config approach (#379)
* Fix paths for bowtie2/build_test

* Fix paths for bowtie2/align

* Fix paths for bwameth/index

* Fix paths for bwameth/align

* Fix paths for multiqc tests
2021-03-24 18:29:41 +00:00
Gregor Sturm
2dba72dd14
Fix a bunch of failing tests after switching to test config (#378)
* Update test for trimgalore

* Fix picard markduplicate test

* Fix tests for picard mergesamfiles

* Fix checksum for markduplicates

* Fix multiplemetrics and wgsmetrics

* Fix checksum for mergesamfiles
2021-03-24 18:28:54 +00:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data (#386)
* Adding tar.gz kraken2 db to test data

* Update test path files for untar module

* Update test path files for kraken2/run module

* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
pericsson
1e4fa57139
Update restructured paths (#380)
* dsh filterbed path updated

* dsh splitbed path updated

* adapterremoval path updated
2021-03-24 18:26:54 +00:00
Anthony Fullam
c5a5e25129
Update test data paths. (#375)
* Updata test data paths.

* Remove quote

* Revert quast

* Fix broken test

* Update md5
2021-03-24 18:18:01 +00:00
arontommi
d162f21ab3
Update samtools modules with config logic (#381)
* fixing paths for test

* fixing paths for test

* fixing pats to tests

* fixing paths to tests

* fixing paths to tests

* fixing paths for tests

* fixing paths for tests

* fixing paths for tests

* fixing paths fro tests

* fixing paths for tests

* indentation fixes

* typo

* renaming test results according to new file name

* replacing the md5sums

* fixing brackets

* replacing md5sums

* fixing md5sums

* fixing md5sums'

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Ramon Rivera <riveravicens@gmail.com>
2021-03-24 18:15:30 +00:00
Mark-S-Hill
889465cb2b
update test data paths (#373)
* update test data paths

* Update test md5sums

* gatk test fixes & update variantfiltration main

* few extra fixes after review

* fix suspected format error

* Update software/gatk4/variantfiltration/main.nf

* Update software/gatk4/variantfiltration/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
Kevin Menden
04c3684db7
Fixing a bunch of module tests (#370)
* 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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:36:29 +00:00
Alexander Peltzer
0337916f8a
Add YARA module (#353)
* Initial work on yara module

* Adding in index basics

* Updated the index stuff

* Adding in proper tests

* Fix editorconfig

* Odd paths

* that should do it

* Fix tests

* Fix tests

* FFS

* Once more

* Mapping is not deterministic
2021-03-24 17:14:52 +01:00
Maxime Borry
cfc94b96dd
modify fastp tests (#367)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-24 17:08:59 +01:00
FriederikeHanssen
86df111707
Seqkit/split2 test path update (#372)
* Update test path

* Fix bracket

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:05:43 +01:00
Harshil Patel
c7155d023e
Update bedtools modules with config logic (#369) 2021-03-24 14:14:19 +00:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests (#365)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint

* Initial commit for test data config

* Rename test data

* Include test config

* Update indents

* Update test for FastQC via config

* Remove quotes of bottom-level variables

* Use underscores in key names

* Get tests working for fastp

* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Gisela Gabernet
22eaefe583
Add module kallisto/index (#357)
* add kallisto index module

* update kallisto module

* add kallisto module tests

* update kallisto index test.yml

* update test data paths

* fix version

* fix kallisto index test yml

* remove TODOs

* Update software/kallisto/index/main.nf

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

* Update software/kallisto/index/main.nf

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

* output folder instead

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data (#354)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Yuk Kei Wan
323856a9da
add nanopore 100-read test subset (fast5, fastq, and bam/bai) (#344) 2021-03-24 05:13:34 +00:00
arontommi
86bb832fae
Strelka germline (#340)
* nf-core template created

* boilerplate and sarek_dsl2 code merged

* adding an option to give it args

* bai got away

* seperating vcf files and vcf index files into seperate streams

* some minor spacefixes

* adding standard information about the module

* removing typos

* some basic tests based on tiddit tests

* removed the bed parameter, should be provided via options.args instead

* removing typos

* adding indexed bam file instead

* Adding changing out fasta with reference to deal with empty fasta input

* adding the correct fasta

* removing the empty test

* adding the correct data to the testoutput and removing the md5sum since
it constantly changes

* adding  target_bed to input

* adding info on target bed

* adding target bed to test

* adding more files to the test

* adding meta for target bed test

* adding a test for target_bed

* typo

* fixing pytest with master
2021-03-24 05:07:29 +00:00
Erkison Ewomazino Odih
67b3e00f58
add flash module (#341)
* add flash module

* remove todo

* run tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
Ravneet Bhuller
a70abc236b
PR for sequenzautils/gcwiggle (#345)
* added files

* edited files

* edited files

* edited file

* test(sequenzautils): Remove md5sum

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
Robert A. Petit III
3f14b1fabe
Update shovill module (#337)
* add shovill module

* removed deprecated shovill module

* fix line ending in functions.nf

* fix yaml indentation

* reduce spades memory usage

* update md5sums

* remove non reproducible md5sum

* Update test.yml

Remove last non-reproducible md5sum.

* purely cosmetic order change

* proper process label, improve output readability

Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) (#302)
* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update pytest_software.yml

* Update main.nf

* fix linting error

* Delete test.yml

* Create functions.nf

* Update main.nf

* change test data

* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Mark-S-Hill
399b58043d
add vcftools module (#334)
* add vcftools module

* fix padding issue

* fix linting errors
2021-03-24 04:54:23 +00:00
Kevin Menden
fe8a783cef
Homer (#330)
* started with homer

* added tests for homer annotatepeaks

* fix md5

* remove md5 sum
2021-03-23 11:24:54 -07:00
Gregor Sturm
e33860a2e8
Prodigal (#333)
* WIP add prodigal

* Implement module and add tests

* Fix EC lint
2021-03-23 11:03:58 -07:00
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
suzannejin
d6850f8312
modified the samtools/fastq module (#339)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
2021-03-23 17:43:52 +00:00
yocra3
5e3c9dfbf0
Add gatk4/baserecalibrator (#327)
* Add gatk4 BaseRecalibrator

* Solve format in main.nf

* Correct functions

* Add pytest
2021-03-23 18:32:37 +01:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) (#301)
* Adding in optitype prototype (To be worked on these days)

* I've tried my best 😆

* No idea

* Add in YML stuff

* Fix paths

* Ok, lets try this

* Adding proper options

* Replacec configbuilder thing

* Fix seq_type

* Adding human bam - sarscov doesnt work

* Fix a bunch of things

* -def

* Make this test run

* Fancy as fuck

* Update tests/software/optitype/test.yml

* Add proper tag

* Remove md5sums

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
Anthony Fullam
3d720a24fd
Add alleleCounter module (#313)
* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Remove newline

* Fix pytest_software.yml

* Update pytest_software.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 14:37:53 +01:00
yocra3
614d61dc13
Add gatk4/applybqsr (#331)
* Add applybqsr module

* Solve problem in functions.nf

* Add to pytest
2021-03-23 14:15:26 +01:00
suzannejin
9115c12f88
new module: samtools/fastq (#316)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
yocra3
569ff03af9
Add readgroup to bam files (#324)
* Add readgroup to bam files
Add recalibration table

* Solve README.md issue
2021-03-23 11:59:49 +01:00
Robert A. Petit III
c2aa95cb6c
add prokka module (#298)
* add prokka module

* adjust test outputs

* fix prokka command

* adjust test outputs

* handle optional input

* update pytest

* update pytest

* adjust test outputs

* adjust test outputs

* switch to lists for optional inputs, add md5sums for non-timestamped outputs

* add optional prodigal training file

* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module (#173)
* Normal bam file added

* Normal bam.bai file added

* Tumour bam bai files added

* human dir added

* annotation dir added

* cnvkit dir added

* cnvkit dir added

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* changed input filenames

* edited main.nf

* edited main.nf

* edited meta.nf

* edited test.yml

* filters.yml

* edited main

* edited main

* edited meta

* edited meta

* edited main

* removed unwanted lines

* edited the path to the main.nf

* removed function.nf

* added functions.nf

* deleted 2 workflows and craeted a common workflow

* deleted paths for 2 workflows and created paths for a common workflow

* Deleted annotation dir

* deleted params.modules

* Edited meta.with_normal

* deleted normal_280_sub_chr21.bam

* deleted normal_280_sub_chr21.bam.bai

* deleted tumour_278_sub_chr21.bam

* deleted tumour_278_sub_chr21.bam.bai

* Edited input and script parts

* Edited input part

* Added

* Edited args

* Edited script

* Edited input

* Changed annotation to annotationfile

* Changed description of the tool

* edited singularuty container

* edited input

* line 44 removed trailing whitespace

* Edited addParams

* Deleted pdf output

* Deleted pdf output

* edited the path to main.nf

* edited path to the main.nf

* Added docker image version

* Removed extra ../

* added md5sums

* added md5sums

* Update software/cnvkit/main.nf

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

* Update software/cnvkit/main.nf

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

* Edited the script

* Edited the input

* Edited main.nf

* Edited main.nf

* edited md5sum for reference.cnn

* removed human fasta

* removed human fasta.fai

* added GRCh38 fasta

* added GRCh38 fasta.fai

* added hg19 fasta.fai

* added hg19 fasta

* Edited fasta file name

* Edited bed file names and md5sums

* Edited md5sums

* edited the input and script section

* edited input section

* added targetfile

* changed the files

* changed the output files

* added bam files

* added bam files

* remove files

* added md5sums

* replace file

* added files

* edited tests/software/cnvkit files

* edited tests/software/cnvkit files

* edited authors list

* removed files

* added files

* added files

* added files

* added files

* added file

* added file

* added file

* added file

* edited files

* edited files

* edited files

* edited files

* edited files

* edited files

* added new module

* added new module

* edited files

* edited file

* edited file

* edited file

* removed files

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 (#311)
* Inital nf-core create

* remove TODO comments, input and output files defined

* add get version in script

* added flow control for single/paired end data

* added script main commands

* removed completed TODO messages

* removed completed TODO messages

* added software info

* added input reads description

* added output description

* added description and keywords

* added single end test

* added paired end test

* fixed sample name flag

* fixed reverse read variable

* added test yaml

* update for pytest_software

* order in pytest_software was different

* replaced functions.nf with copy from another module

* simplify read command line

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

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Garcia
0a4fa5050a
Update main.nf (#314) 2021-03-22 17:16:43 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval (#309)
* add adapterremoval module

* fix indentations

* switch to process_medium

* update docker tests

* remove duplicated entry

* fix line ending

* Update software/adapterremoval/main.nf

* Update software/adapterremoval/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00