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1871 commits

Author SHA1 Message Date
Robert A. Petit III
51f2d9a806
Update main.nf (#938)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:47:41 +01:00
Robert A. Petit III
b5b3ff16ce
add module for fastq-scan (#935)
* add module for fastq-scan

* change fastq to reads

* remove uncompressed support

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:41:36 +01:00
Robert A. Petit III
7be60774b6
add module for tbprofiler (#947)
* add module for tbprofiler

* Update test.yml

* Update meta.yml

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:35:55 +01:00
James A. Fellows Yates
2c3c87a10f
Add leehom module (#1052)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add leeHom module

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:26:06 +01:00
Benjamin Wingfield
b012b349c1
New module: plink2/vcf (#1006)
* implement plink2 VCF import

* fix yaml indentation

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 13:55:18 +00:00
Ilya Pletenev
c48244b677
Add new module 'ataqv/ataqv' (#998)
* Add new module 'ataqv/ataqv'

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
Daniel Straub
661bdb645e
Change Spades input (#1039)
* Change spades module

* correct meta map description

* adjust memory handling

* remove trailing whitespace

* fix hmm input

* Update modules/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:53:07 +00:00
Daniel Straub
171a2a2dbf
Unicycler with long read input (#1041)
* Unicycler with long read input

* tests and md5sums

* remove unstable md5sums

* Update modules/unicycler/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:48:56 +00:00
JIANHONG OU
9475960928
Bwa index (#1040)
* fix a bug that the prefix is not handled by index.

* build the test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:26:01 +00:00
alexandregilardet
94851901d5
add new module pmdtools/filter #847 (#963)
* commit but won't be used because pmdtools should have a submodule

* added submodule pmdtools/filter

* removed pmdtools module created before deciding to design two submodules

* oops forgot to remove a TODO

* removed white space meta.yml, removed v in version and manually added submodule /filter to test

* Update pytest_modules.yml

* Update main.nf

added split_cpus for multi-tools module resources

* Update test.yml

added .pmd extension to match modules/ main.nf

* Update test.yml

update md5sum

* Update singularity and docker build in main.nf

From build 4 to 5 in order to match the conda one

* Update modules/pmdtools/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pmdtools/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update main.nf adding samtools version

we need both pmdtools and samtools versions

* Update main.nf remove .pmd extension

* Update test.yml md5sum

Because file extension changed

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
Sébastien Guizard
001d5071c2
Update: gstama/collapse (#1057)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

* 👌 IMPROVE: Update to gs-tama 1.0.3

* Update modules/gstama/collapse/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:57:55 +00:00
Sébastien Guizard
ec15d0f9fd
Update module: pbccs (#1018)
* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

* 🐛 FIX: Update meta.yml

* 🐛 FIX: Update reports filenames with chunk number.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:19:26 +00:00
Maxime U. Garcia
3b600af50e
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059)
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0

* update md5checksum

* commit all files

* actually checksum was good, but I suspect something fishy with the tests
2021-11-11 08:58:59 +01:00
Robert A. Petit III
4bd530135f
add ngmaster module (#1024)
* add ngmaster module

* add docker container

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 11:25:50 -07:00
Maxime Borry
56d5eb9834
Add Bacillus fragilis alignments to test_data.config (#1054)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* add bacillus fragilis alignments

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 17:40:07 +01:00
Maxime U. Garcia
64006e239a
fix: actually do the tests for multiple files (#1058) 2021-11-10 16:26:34 +01:00
Maxime Borry
24707f2144
Fix read indexing in AdapterRemoval module (#1051)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* fix read index

* update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 12:21:12 +00:00
Daniel Lundin
8b4bfb12bb
Add log to output from bbmap/align (#1050) 2021-11-10 10:27:52 +00:00
Mei Wu
7fdeed5b79
Picard/collecthsmetrics (#927)
* added template

* integrated module

* added fasta index info

* test works, have placeholder data for baits until test-data PR is merged

* added new files to config

* updated test files

* fixing fails 

* okay final fix here on the md5sum :face_palm:

* md5sum variable

* update meta.yml to reflect consistency to main.nf

* reverted version so conda works

* Apply suggestions from code review

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* md5sum can't be generated consistently for output

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-10 10:52:54 +01:00
Maxime U. Garcia
1abe23e159
Add CRAM to samtools/index (#1049)
* feat: update samtools/index

* feat: add test

* fix: lint

* fix: output file + md5
2021-11-10 10:30:48 +01:00
Maxime Borry
b399f22af2
Add new module: cmseq/polymut (#918)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* first cmseq commit

* compressing and removing not reproducible md5sums

* save intermediate work

* follow symlinks while decompressing

* add cmseq/polymut

* add polymut

* add extra test with optional input file

* remove metabat2

* Update modules/cmseq/polymut/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/cmseq/polymut/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/cmseq/polymut/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* fix file extension

* Update modules/cmseq/polymut/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add test without bam index

* split tests in workflows

* answer PR review

* report version from variable

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 16:12:51 +01:00
Benjamin Wingfield
6bb4a6a7ee
Implement plink/extract module (#901)
* Implement PLINK_EXTRACT module

* fix plink version number

* Update main.nf

* Update test_data.config

* Update modules/plink/extract/main.nf

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

* just use one channel

* fix test with new channel input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 14:03:13 +00:00
anan220606
6d3d8306e1
Add new module Mapdamage2 (#975)
* Fitst attempt at mapdamage2

* Add new module mapdamage2

* Removed __pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify meta.yml

* Update pytest_modules.yml

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* edit the meta.yml and main.nf after reviews

* Update meta.yml

* Update meta.yml

Co-authored-by: AIbrahim <AIbrahim@apate.hki-jena.de>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-09 14:05:23 +01:00
GCJMackenzie
e0ab4ff4ff
bugfix: panel of normals subworkflow: remove md5sum on a gzipped file (#1045)
* commiting changes to switch branch

* commit to setup remote branch

* first draft of the sompon workflow

* keep branch in line with gendb bugfixing

* Update test.yml

* tidy up main.nf

* fixed md5sum

* Update test.yml

removed md5sum from test_panel.vcf.gz.tbi

* Update test.yml

* remove md5sum from gzipped test_panel.vcf.gz.tbi

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-11-09 11:08:59 +00:00
GCJMackenzie
9573cb1bec
Add panel of normals subworkflow (#1044)
* commiting changes to switch branch

* commit to setup remote branch

* first draft of the sompon workflow

* keep branch in line with gendb bugfixing

* Update test.yml

* tidy up main.nf

* fixed md5sum

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-11-09 10:16:43 +00:00
Maxime Borry
e0ada7d219
New module: metabat2 (#875)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 21:08:26 +01:00
Robert A. Petit III
c10f9eb817
add lissero module (#1026)
* add lissero module

* Update test.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:52:07 +01:00
Robert A. Petit III
8ca8da46c2
add emmtyper module (#1028)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:43:15 +01:00
GCJMackenzie
316aedaaa6
bug fixes: genomicsdbimport (#1035)
* saving changes to checkout

* saving to sort out other branch

* removed yml tracking of files that cant be tracked due to directory name changing between runs

* test data added, ready for pr

* fix eol linting error

* Update modules/gatk4/genomicsdbimport/main.nf

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* merging with master

* update push to show progress

* tests now working untar able to pass data to genomicsdbimport

* commit to checkout

* tests updated, module reworked to simplify and emit updated gendb

* Apply suggestions from code review

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

* update meta.yml 

Priority of input options changed, updated to reflect this

* Update test.yml

name prefix changed in main script, test.yml updated to reflect this

* fix tests due to review changes

* bug fixes, multicalling samples and gendb emissions now fixed

* Update pytest_modules.yml

* Update meta.yml

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 15:51:15 +00:00
Robert A. Petit III
729d9ae450
add meningotype module (#1022)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:44:26 +01:00
Robert A. Petit III
22aa168622
add scoary module (#1034)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:34:39 +01:00
Phil Ewels
02932973fa
bwameth: Add touch command to fix problem with bwameth rejecting older files (#1037)
See https://github.com/nf-core/methylseq/pull/217 for context where this fix was added into the DSL1 methylseq pipeline.
2021-11-06 16:05:04 +01:00
Lasse Folkersen
e560fbbc3e
Imputeme (#882)
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.


Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-11-05 10:25:54 +01:00
Francesco L
02892ef654
New module: Samblaster (#954)
* add base code from samblaster

* added test yml

* fixing versions files, should this be the cause of online lint failures

* removed tmp files that shouldn't be there

* fixing output file name - 1

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

* fixing output file name - 2

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

* fixing output file name - 3

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

* fixing output file name - 4

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

* fixing output file name - 5

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

* fixing output file name - 6

* fixed indent

* fixed input name and updated test.yml file with new name

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-04 18:18:56 +01:00
Robert A. Petit III
fc4f3e8822
add seqsero2 module (#1016)
* add seqsero2 module

* correct lint errors

* Update modules/seqsero2/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* set output directory

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-04 07:49:30 +00:00
James A. Fellows Yates
08b71fa85f
New module: gunc run (+ gunc downloaddb) (#880)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add GUNC download_db and run commands

* Bump with version without zgrep

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Harshil formatting

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-03 17:01:23 +01:00
Maxime U. Garcia
11226d9d98
fix remove md5sum check (#1017) 2021-11-03 11:41:12 +01:00
Maxime U. Garcia
9767b081b9
Merge freebayes subtools (#1015)
* feat: merge freebayes subtools

* fix: typo

* assess comments from review

* fix: path to module
2021-11-03 11:22:06 +01:00
fbdtemme
4619d012e5
Add cram support to Allelecounter module (#1013)
* Add CRAM support to allelecounter

* Update meta.yml

* Rename bam,bai to input,input_index

* Apply suggestions from code review

* Fix reference to renamed variable

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-02 17:00:25 +01:00
Simon Pearce
374d81e0b3
readcounter module for hmmcopy (#1001)
* readcounter module for hmmcopy

* Changed version number

* Fix indentation

* Update main.nf

* Update modules/hmmcopy/readcounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 11:01:13 +00:00
Simon Pearce
cac6dc83bb
gccounter module for hmmcopy (#1003)
* hmmcopy gccounter working

* Update modules/hmmcopy/gccounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

* Update main.nf

Changed version to 0.1.1 as the container says

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 09:59:25 +00:00
Simon Pearce
81d65d4978
Samtools fixmate module (#991)
* Samtools fixmate module

* Update modules/samtools/fixmate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/samtools/fixmate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update main.nf

* Update modules/samtools/fixmate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update meta.yml

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-01 12:12:14 +00:00
Harshil Patel
9fb26ae462
Add IDR module (#908)
* Add IDR module

* Add meta and implement main todos

* Modifying idr tests

* Update tests/config/test_data.config

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

* Update tests/config/test_data.config

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

* Update main.nf

* Update tests/config/test_data.config

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

* Update test with new file name

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-30 10:52:13 +02:00
GCJMackenzie
bc8697b766
FIX: Createsomaticpanelofnormals add requested test changes (#983)
* files created for createsompon, script written, meta written, still needs tests

* updated to 2.0.0 method input, however this requires a genomicsDB input now

* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests

* versions updated, issue with test data not able to download directory

* updated tests to include repo-side data

* Apply suggestions from code review

* Update modules/gatk4/createsomaticpanelofnormals/main.nf

* temp commit to allow checkout

* updated createsompon tests to use tarred gendb

* resolve conflict

* Update tests/modules/gatk4/createsomaticpanelofnormals/main.nf

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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:45:32 +01:00
GCJMackenzie
7afb962f0b
New module genomicsdbimport (#857)
* saving changes to checkout

* saving to sort out other branch

* removed yml tracking of files that cant be tracked due to directory name changing between runs

* test data added, ready for pr

* fix eol linting error

* Update modules/gatk4/genomicsdbimport/main.nf

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* merging with master

* update push to show progress

* tests now working untar able to pass data to genomicsdbimport

* commit to checkout

* tests updated, module reworked to simplify and emit updated gendb

* Apply suggestions from code review

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

* update meta.yml 

Priority of input options changed, updated to reflect this

* Update test.yml

name prefix changed in main script, test.yml updated to reflect this

* fix tests due to review changes

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:21:34 +01:00
FriederikeHanssen
3df4fe6085
add freebayes/somatic and update freebayes/germline (#990)
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00
Jose Espinosa-Carrasco
0a7368aa6f
Refactor genrich to avoid params in main (#981)
* Refactor genrich to avoid params in main

* Missed to commit test.yml file
2021-10-29 16:37:39 +02:00
louperelo
a4943a9e57
Mtnucratio (#986)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* add new module mtnucratio

* fix main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* layout in main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-29 15:02:02 +02:00
avantonder
977d96ed0b
Add Racon module to nf-core/modules (#949)
* add racon

* add racon

* add racon

* add racon module

* add racon module

* edit racon module

* edit racon module

* edit racon module

* edit racon module

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-10-29 13:33:38 +01:00
Chris Cheshire
2959b4ba07
Bedtools sort add extension choice input (#984)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Added extension input for bedtools sort

* whitespace

* Updated docs

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
2021-10-29 13:22:17 +01:00