Commit graph

1792 commits

Author SHA1 Message Date
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
Francesco L
460a3ed87b
Fgbio group reads by umi (#952)
* adding template for module groupreadsbyumi

* update modules with code

* strategy is required argument so moving it to input rather than options.args

* tests successful committing yml

* added meta to output

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 14:00:54 +02:00
Daniel Lundin
84cb78cc98
Khmer normalizebymedian (#985)
* Templates for new module

* pe only test passing

* only_pe and only_se passing

* only_pe, only_se, mixed passes

* Multiple pe + se tc passes

* Passing args works

* Add 'interleaved' to description

* Fixed linting message

* Update modules/khmer/normalizebymedian/main.nf

Good point.

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2021-10-29 13:23:34 +02:00
FriederikeHanssen
ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

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

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +02:00
GCJMackenzie
71945a5b5f
Mutect2 add mitochondria mode and update tests (#967)
* new mitochondria mode added, tests updated to allow for temp fix for test data

* add cram test

* bam/bam_idx renamed to input and input_index

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-10-29 11:27:56 +01:00
Francesco L
4b8c7ac7bd
Bam2fq (#958)
* added template for module

* update main

* added specific code

* wrong variable name in else script

* added tests for both split and nosplit

* docker test successful - updating yaml

* adding echo to version print
2021-10-29 10:46:34 +02:00
Sateesh
5b1fe84bc6
add new assembly scan module (#971)
* add new assembly scan module

* add newline endings

* fix newline ending

* add newline at end

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 10:01:23 +02:00
Chris Cheshire
e8b33e6eb1
bedtools/genomecov updated to allow for providing a per-sample scale factor (#799)
* 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 genomecov scale module

* Updated tagging

* Removed extra module - began merging

* Removed extra module tests

* Updated genomecov to take a scale value

* Updated line endings

* Removed redundant test

* Update tests/modules/bedtools/genomecov/main.nf

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

* Added checking for existing -bg arg

* Update modules/bedtools/genomecov/main.nf

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

* Update modules/bedtools/genomecov/main.nf

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

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-28 17:50:25 +01:00
FriederikeHanssen
1662201102
Add gatk4/estimatelibrarycomplexity (#965)
* Add gatk4/estimatelibrarycomplxity

* forgot to add yml

* Fix placeholder
2021-10-28 17:49:27 +02:00
emnilsson
9402595711
New module seqtk/mergepe (#951)
* First step into creating a seqtk/mergepe module to interleave fastQ input

* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task

* Modifications to test the new seqtk/mergepe module.

* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work

* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.

* Fix trailing whitespaces

Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
2021-10-28 16:53:33 +02:00
Jose Espinosa-Carrasco
fd1189c2f5
Updating test file for optitype (#782)
* Provide an exisiting bam file for optitype

* Update main.nf

Attempt at fixing this with new testing data

* Trying slightly different approach

* Mini fixes, not sure whats wrong here

* Add bam file with NM tags in all reads for optitype

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
2021-10-28 14:24:52 +02:00
Gisela Gabernet
d5183a7fec
new module cellranger mkref (#896)
* add cellranger mkref module

* add cellranger mkref tests

* update test yml chksum

* fix module linting

* fix test yml

* fix getprocessname

* fix versions typo

* fix cellranger test.yml

* fix versions.yml

* test versions.yml

* fix grep version

* fix cellranger version

* add dockerfile and readme

* review container statement

* Update modules/cellranger/mkref/meta.yml

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

* add disclaimers

* change location dockerfile

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-28 13:33:57 +02:00
Gisela Gabernet
0b0f87c2f7
add porechop module (#914)
* add module main porechop

* update porechop main

* add porechop functions

* update meta porechop

* add test main porechop

* add porechop pytest yml

* add porechop test.yml

* Update modules/porechop/meta.yml

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

* re-add porechop avoid conflict

* Update modules/porechop/meta.yml

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

* fix prefix suffix

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-10-28 13:21:36 +02:00
louperelo
263bbe56d2
add new module samtools/depth (#950)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* Apply suggestions from code review

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-28 12:53:21 +02:00
James A. Fellows Yates
e27553b989
Add module: dedup (#907)
* 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 dedup (tests and version not working)

* Fix dedup and tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-28 12:10:21 +02:00
Francesco L
a0bc08732c
Rewritten module fgbio/fastqtobam (#916)
* added template for fastqtobam

* porting old code into new template

* update with missing getprocessname function

* test completed - updating all

* fixed linting issues

* improved reading

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

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 19:06:06 +02:00
Maxime U. Garcia
80d8e87fa4
adding new manta/germline + manta/tumoronly modules (#906)
* feat: all manta/single to modules

* fix module name

* fix module name

* fix: changes from review comments

* fix: test data
2021-10-27 18:24:48 +02:00
FriederikeHanssen
257078bb39
Update strelka, by enabling BP if Manta candidates are present (#923)
* add BP to strelka/somatic

* merge conflicts

* update strelka modules for BP

* update strelka modules for BP

* apply suggestions from code review
2021-10-27 17:49:54 +02:00
Daniel Straub
12a3f80f33
add filtlong (#919) 2021-10-27 17:00:11 +02:00
FriederikeHanssen
754db250a0
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)
* remove params statement

* add manta/somatic module

* fix strelka target bed thing

* removing checksums should make this pass

* Update modules/manta/somatic/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fix indentation

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 16:14:52 +02:00
Matthias Hörtenhuber
b552958341
add paraclu (#909)
* add paraclu

* remove TODOs

* add min_cluster as input parameter, remove option parameters

* add tool_dev_url
2021-10-27 15:48:49 +02:00
Gisela Gabernet
f47c27edfb
Update checksum modules using human GTF (#900)
* update test yml star align

* update test yml stringtie merge

* update star genomegenerate yml

* update test yml rsem calculateexpression

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 23:09:04 +01:00
James A. Fellows Yates
bd2baa1e7c
New module: maxbin2 (#895)
* 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

* Added, just need to finish tests once we have bacterial data

* Add prelim test data

* Fix version reporting

* Add tests based on proposed test-dataset

* Finalise new testdata

* Fix md5sum issue by removing it...

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-26 22:07:33 +01:00
James A. Fellows Yates
a740a6ff48
New module: checkm/lineagewf (#899)
* 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

* Added but test failing due to null on output channel

* fix prefix variable

* Complete checkm_lineagewf

* Remove TODOs

* Add description of fasta_ext parameter

* Improve meta map for this context

* Update meta.yml

* Update modules/checkm/lineagewf/meta.yml

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

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 21:54:10 +01:00
Gregor Sturm
2ad98162f3
Notebook modules (#617)
* Draft rmarkdown module

* stub jupyter notebook module

* Create yaml file with params

* Update meta.yml for rmarkdown module

* Add comment on YAML

* Update notebooks module, clean up parametrize.nf

* Two separate channels for parameters and input files

* Fix Rmd render script

* Add tests for rmarkdown

* Fix tests for rmarkdown module

* Update checksums

* Fix tests for jupyter

* Test without Grab()

* Update software versions

* update rmarkdown dependencies

* Draft for multiple versions

* Fix indent of script

* Fix indent in rmarkdown script

* Emit version.syml

* Update modules/rmarkdown/main.nf

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

* Update modules/rmarkdown/meta.yml

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

* Update modules/rmarkdown/meta.yml

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

* Rename rmarkdown to rmarkdownnotebook

* Add rmarkdown mulled biocontainer

* Write sessionInfo to separate log file

* Update rmarkdownnotebook

* Sessioninfo does not have a stable md5sum

* Update jupyternotebook

* Update meta

* Add jupyternotebook biocontainers

* Handle Groovy Gstrings in parameterize

* Update to versions.yml

* Update functions.nf

* Fix versions yaml

* Fix EC lint

* Update modules/rmarkdownnotebook/main.nf

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

* Update modules/jupyternotebook/main.nf

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

* Use official test data

* Harshilify

* Make parameters channel clearer

* Apply suggestions from code review

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

* Apply suggestions from code review

* Update main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-24 20:51:56 +02:00
Sébastien Guizard
0a5ddd0ad0
Update module: bamtools/split (#885)
* 👌 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 bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 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 bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* Update modules/bamtools/split/meta.yml

Add bam, split, chunk tags

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

* 🐛 FIX: Correct meta.yml

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Update test.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:39:27 +01:00
GCJMackenzie
3c8ca3fec4
Createsomaticpanelofnormals (#859)
* 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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:30:14 +01:00
Sébastien Guizard
8524e6b40f
Update of pbccs (#835)
* 📦 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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:09:41 +01:00
Sébastien Guizard
d3369789da
New module: gstama/merge (#813)
* 👌 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 bamtools module

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE : add test bed files

* 📦 NEW: Add gstama/merge module

* 🐛 FIX: Change process label

* 👌 IMPROVE: do not merge empty bed

* 🐛 FIX: Change 0 lines files detection

* 🐛 FIX: replace spaces by tab

* 🐛 FIX: Remove tuple for report channel and add version output channel

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fix Typos

* 👌 IMPROVE: Updates + clean code

- Update to last versions.yml file
- Better output channels
- Update meta.yml

* 👌 IMPROVE: Correct typo

* 👌 IMPROVE: Remove included filelist creation and add an input channel

* 🐛 FIX: Correct typo

* 👌 IMPROVE: Add filelist file

* 🐛 FIX: tama_merge.py emit a version number

* Update modules/gstama/merge/meta.yml

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

* 👌 IMPROVE: Update meta.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:00:39 +01:00
Sébastien Guizard
481d3c811d
New module: gstama/collapse (#809)
* 👌 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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:55:28 +01:00