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* New module for the cram-size command of samtools. * Update modules/nf-core/samtools/cramsize/main.nf Adding name of the tool Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/samtools/cramsize/main.nf Adding prefix to make the module set up more flexible. Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/samtools/cramsize/main.nf Changing `.baseName` by `prefix` in output names. Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Stub added to the main.nf script. * Adding generated test.yml file. * Adding pytest. * Adding a new nf-core module called plasflow. * Update manta modules (#3615) * Update manta somatic * Update manta tumoronly * add varlociraptor call subcommand (#3529) * add call subcommand * at calls runs now [skip ci] * add test files * linting * fix tests * add contains check * Update tests/modules/nf-core/varlociraptor/callvariants/main.nf Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se> --------- Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se> * add new module iCount-mini/metagene (#3612) * add module template * first version * update testing and linting * update file naming * update test * fix test * Newmodule ngmerge (#3626) * ngmerge first commit * main module code * complete module * remove trailing whitespace * fix versions.yml * fix version yml * versions yml * vyml * try vyml again * touch versions yml * vyml * NEW MODULE: PURECLIP (#3624) * initial commit * module version 1 * full testing * linting * fix version yaml * fix version yaml command * fix version yml maybe this time please * fix version yml for real this time * try again versions yaml * fix version yml * vyml * version yaml * vyml * update ref to have meta * fix integer overflow (#3620) Co-authored-by: Steven Strong <steven.strong@adelabio.com> * Fix metaeuk_easypredict when using mmseqs database (#3525) Fix metaeuk and add tests * 3630 add unstitched reads as emitted output of ngmerge (#3632) * add -f option * update tests * Update vardictjava (#3633) * new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * update vardictjava * Adding modules from #scrnaseq for simpleaf (#3619) * Start adding modules from #scrnaseq for simpleaf * Fix tests * t2gene is necessary, simplify tests * Linteing fixes * Fix test files * Test fixes * prettier * Address feedback * Update test string- logs in newer version lack some messages * Apply suggestions from code review Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Post-review index fixes * Post-review quant fixes * add stubs * Add metas, fix meta usage * Appease eclint --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * update icount mini version (#3640) module currently fails, i've fixed the error in icount-mini so now by bumping the version here we fix the issue (old matplotlib syntax) * Bump taxpasta version (biocontainer not yet available) (#3639) * Purecn/run (#3140) * Set up nf-core template for purecn/run module * Add run script and I/O * Clean TODOs and set main script * Fix duplicate entry * Set up main script * [ci skip] Format with prettier * [ci skip] Address review question and set up stub * [ci skip] Set stub for testing * Reformat with prettier * [CI skip] Adjust some typos * [CI skip] Set up test script using stub * Set up test yml * Reformat with prettier * Set up meta.yml file and fix typos * Reformat with prettier * Fix typo * Remove quay.io from container string * Remove optional input argument * Add optional outputs and clean non-mandatory parameters * Clean non-mandatory outputs * Reformat outputs * Fix minor and address reviews * new module: samtools/import (#3642) * new module: samtools/import * fix versions * fix versions some more * Update modules/nf-core/samtools/import/main.nf * fix meta * Adding seqkit sliding command (#3637) * Adding seqkit sliding command * Linting fix * Updating for better matching * reverted to regex using end line markers for better matching other wise fastq gets caught by fa, error in other modules * Added a test for fastq too --------- Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Hicexplorer hicpca (#2933) * create module hicpca * Update modules/nf-core/hicexplorer/hicpca/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update modules/nf-core/hicexplorer/hicpca/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * add more keywords. * remove quay.io. --------- Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Fix bug in pyrodigal module (#3643) Add "--force" to pigz * Update gecco/run (#3652) Version bump to 0.9.8 * New module: instrain/compare (#3623) * Started instrain compare tests * instrain compare * Update modules/nf-core/instrain/compare/main.nf * Update modules/nf-core/instrain/compare/main.nf * Update modules/nf-core/instrain/compare/main.nf * Updated test.yml and added stub * Update modules/nf-core/instrain/compare/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update meta.yml to include meta2 * Updated test.yml output files * Changed md5 to content for several test.yml files * changed content to contains * Added another contains option in test.yml * shortened contains string to pass prettier check --------- Co-authored-by: Margot Lavitt <margotl9@n3065.hyak.local> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update LAST modules to v1453 (#3303) * Update LAST to version 1453. * update lastdb version to 1453 * update last mafconvert to 1453 * update last mafswap to 1453 * update postmask to last v1453 * update last split to v1453 * last update train to v1453 * Update meta.yml Change output value type to string * Update meta.yml Change output value type to string --------- Co-authored-by: Charles Plessy <charles.plessy@oist.jp> Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk> Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp> Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com> * Hisat2-build: index construction w/ truly optional inputs (#3649) * index construction mode dependent on optional inputs rather than memory availability * added tests for new functionality * updated tests to use appropriate test data * cleaned up test.yml to only contain BUILD outputs * removed unnecessary extract ss call * added : to empty metamaps. Reverted to sarscov2 test files --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update metaphlan module (#3661) * CNVKit 0.9.10 update (#3651) * upgrade CNVkit to 0.9.10 * homogenise keywords of all CNVkit modules * Add samtools dependency to bam2seqz module of sequenzautils Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests) * Update cnvkit to 0.9.10 Changes: - Update cnvkit to 0.9.10 - Update samtools in cnvkit modules to 1.17 Based on #3545 authored by @priesgo. * cnvkit 0.9.10 test update * update checksums of output files in tests for CNVkit batch * Update cnvkit/export VCF test * Additional tags for sequenzautils --------- Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com> Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com> * Update gatk3 modules (#3660) * update mapdage2 module * Add meta for all files in gatk modules * Update tiddit to v3.6.1 (#3663) * Update stubs for samtools flagstat (#3657) Update stubs Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se> * R differential modules control over output prefixes (#3664) * R differential modules control over output prefixes * Set differential module prefixes * Actually we need to do prefix handling within the template * Set differential module prefixes * Fix test files for new prefix specification * Add meta to limma test * Fix DESeq2 tests * fix remaining tests for limma * Update grep to fix broken solve * Try bumping affy * Use new build * update md5sum for annotation * Update stubs for samtools idxstats (#3665) * Update stubs * Update stubs for samtools idxstats --------- Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se> * Bump ensembl-vep modules to 110.0 (#3658) * bump ensembl-vep to 110.0 * update tests * put conda tests back * update config for ENSEMBLVEP_DOWNLOAD * update tests for related subworkflows * fix path to module * enable conda tests back * better tests * fix tests * nicer channels * fix channel queue to value * fix syntax * Remove containers with cache with snpEff too (#3670) * update tests for snpeff * remove containers in config * fix cache version in tests * update meta.yml * fix meta.yml * fix meta data * fix md5sum * re-enable conda tests * Update stubs for bwa mem (#3671) Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se> * Additional optional output to homer/annotatepeaks (#3667) * add optional stats output for use with the -annStats parameter (to be provided with ext.args) * Update meta.yml * add additional stats output to annotatepeaks test --------- Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Hisat2 align splicesitesoptional (#3656) * added align tests for splicesitesoptional * changes to homo sap * updated splice sites to be optional with tests * Fix invalid GATK container (#3673) Fix GATK container which was invalid Fixes #3668 * Update: bamtools, gstama, ultra (#3655) * Update Bamtools [2.5.1 -> 2.5.2] * Update gstama/merge [1.0.2 -> 1.0.3] * Update ultra [0.0.4.2 -> 0.1] * Update ultra/index|align|pipeline tests replace gffread by gnu/sort * Irregular md5sum for database.db * Update bamtools/convert test.yml * Fix centrifuge: reduce number of input channels (#3674) * Bump taxpasta version (biocontainer not yet available) * Remove unnecessary (and sometimes problematic) input channel * Improve output glob for optional alignments * Remove now unnecessary variable from command * linting * Add missing args * Remove unused ublast module * Checking tests that were failing from the samtools/cramsize module. * Writing some errors. * Checking failed test of the samtools/cram-size module. * Checking failed test on yml file. * Fixing test.yml file. * Fixing test.yml from plasflow module. * Removing trailing whitespaces from files. * Fixing test.yml from plasflow module. * Removing Plasflow from conda. It doesn't work. * Running prettier on test.yml from plasflow. * Details of the conda environment. * Adding specific Tensorflow version for Plasflow. * Adding channel for python 3.5 * Fixing the channel for python 3.5 for plasflow module. * Changing the channel for python 3.5 (to conda-forge) for plasflow module. * Update cramsize * Excluse cramsize from pytest * Remove plasflow * Update and fix linting * Update modules/nf-core/samtools/cramsize/tests/main.nf.test Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Update modules/nf-core/samtools/cramsize/tests/main.nf.test Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> --------- Co-authored-by: limrp <limrod.15@gmail.com> Co-authored-by: limrp <119093929+limrp@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com> Co-authored-by: Steven Strong <sstrong99@users.noreply.github.com> Co-authored-by: Steven Strong <steven.strong@adelabio.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@healx.io> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Aldo Sergi <50989854+aldosr@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Co-authored-by: Margot Lavitt <margotl9@n3065.hyak.local> Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@gmail.com> Co-authored-by: Charles Plessy <charles.plessy@oist.jp> Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk> Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp> Co-authored-by: Jack Tierney <43453737+JackCurragh@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com> Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com> Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com> Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Ram Sai Nanduri <sai.rama7412@gmail.com> Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se> Co-authored-by: Laura Blum <laura.blum.n@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
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