Merge pull request #990 from mskcc/bugfix/lohhla_readtable_bug

Hotfix/1.4.4

Merge pull request #937 from mskcc/bugfix/oncokb_authentication

hotfix/1.4.3

Merge pull request #929 from mskcc/develop

Release/1.4.2

Merge pull request #914 from mskcc/hotfix/1.4_official

Hotfix/1.4 official

Merge pull request #910 from mskcc/develop

Release/1.4

1. Fixed mapping files megatron list for samples to make them consist…

…ent with LIMS and IGO endpoint #810

2. Added facets qc and use a formal facets-preview container now. #822
3. Enhancements to multiqc report #823
4. Qualimap added to the QC module and multiqc report #824
5. Bugfixing #829 Double memory increase after second time failure for MsiSensor #830
6. Bugfixing in process SomaticCombineChannel #828
7. Bugfixing: for #658 llohhla error cathing #836
8. Bugfixing: modify SomaticCombineChannel and genome RunMsiSensor 4th try mem #839
9. Enhancement: rearrange facets dockers #835
10. Enhancement: tempoSig optional cosmic signature reference version #837
11. Hotfix: raise 4th try memory limit for QcQualimap
12. Hotfix: configure `SomaticCombineChannel` and `GermlineCombineChannel` to use updated container.

Merge pull request #818 from mskcc/develop

Release/1.3.3

Merge pull request #816 from mskcc/develop

Release/1.3.2

Merge pull request #798 from mskcc/develop

Release/1.3.1

1.3 (#765)

* Feature/upgrade delly wf (#753)

* Upgrade delly to 0.8.2 and create new Docker containing bcftools and delly together to remove burden from Delly-Manta merging steps

* added ps to Docker file and soft-linked delly to /usr/bin

* fixed hard-coded reference to delly location, reverted softlink to delly to /usr/local/bin as this was in PATH all along

* moved up output of delly in DAG to avoid nextflow failure

* fixed publishing of delly calls into results folder

* removed originally delly container and insured publish of delly files

* including auxiliary Docker files such as ._Dockerfile

* removed ._Dockerfile files

Co-authored-by: gongyixiao <[email protected]>
Co-authored-by: Anne Marie Noronha <[email protected]>

* add watchPath

* fix bamFiles channel empty

* bamMapping.tsv produce absolute path

* skip header

* standardize aggregate channel names

* combine with cohort channel

* add watch params

* aggregate tag and cohort dir

* fix QcBamAggregate combine

* add pdf.* in .gitignore

* fix comma to semicolon in into

* use params.watch and put watchPath in Utils

* remove params.watchPath from nextflow.config

* remove switches in pipeline.nf

* remove switches in pipeline.nf 2

* move watchPath functions into pipeline.nf

* remove changes in tempoutils

* add support for aggregate cohort tsv

* add support for watch aggregate tsv

* align

* test for aggregate tsv only

* support for watch

* add switches to aggregate

* remove duplciated line

* remove duplicated lines2

* add back QcBamAggregate support

* Update running-the-pipeline.md

* Update running-the-pipeline.md

* Update outputs.md

* Update outputs.md

* Update running-the-pipeline.md

* use splitCsv

* change cohortSize to be integer

* remove duplicates

* use splitCsv for watchPath

* add pairingQc switch for QcConpair and aggregate

* add unique after the groupKey

* remove the possibility of duplicate

* move RunNeoantigen before SomaticFacetsAnnotation

* change max time to 31 days

* update containers only

* change the max time to 500 hours

* fix bug when two final mafs in one germline combined_mutations folder

* fix GermlineAggregateSv duplicates

* fix index

* fix the facets-suite version

* install facets-suite

* add back install facets

* change DoFacets to use wrapper

* change summarize_project.py path

* facets suite container fix

* update annotate-withzygocity scripts

* make SomaticFacetsAnnotation work

* fix missed change in annotate with zygosity somatic R

* remove _em

* change output channels for arm gene level

* pipeline.nf

* change MetaDataParser to be compatible with facets-suite 2.0

* change metadataparser container version in conf

* fix SomaticAggregateFacets

* make facets output structure compatibale with facets-preview

* Revert "move RunNeoantigen before SomaticFacetsAnnotation"

* add back changes from PR 758

* docs changes

* fix resource genome config

* fix wgs different values

* fix wgd 2

* fix bugs in QcBamAggregate and Facets

* fix 756

* fix bug when _L001_R1_001 and _L001_R1_002 are in fastq files

* add check for R1 and R2 order when merging two channels

* update container

* change geneLevel.R in pipeline.nf

* fix typo

* add data folder

* fix typo

* remove mkdir data

* change directory

* improve splitLanes

* initialize pairingQc variable and set pairingQc to true when --QC parameter is indicated

* fix facets seed random error (#782)

* fix facets seed random error

* added retry limit for DoFacets within script chunk to try up to 4 different seeds in one task attempt

* fixed typo in DoFacets bash script for calling a bash variable

* raise resource usage on DoFacets process to avoid failure due to memory limit

* changed the resources for do facets to 1 cpu x 20 Gb mem for juno and aws profiles

Co-authored-by: Anne Marie Noronha <[email protected]>

* fixed bam truncation bug by using beforeScript and catch_USR2 (#767)

* fixed bam truncation bug by using beforeScript and catch_USR2

* move beforeScript into juno.config to fix travis

* fix close brace after beforeScript

* a working solution for catch USR2

* Bugfix/final touchup1.3 (#790)

* double Neoantigen retry memory increase

* disable lohhla by default

* docs revise

* added similar note on disabling of lohhla to "bioinformatic-components.md"

* fixed redundant text in "variant-annotation-and-filtering.md"

Co-authored-by: Anne Marie Noronha <[email protected]>
Co-authored-by: anoronh4 <[email protected]>

Co-authored-by: anoronh4 <[email protected]>
Co-authored-by: Anne Marie Noronha <[email protected]>