prep 1.3.1 release in develop#799
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gongyixiao merged 3 commits intodevelopfrom May 15, 2020
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* 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 <5620765+gongyixiao@users.noreply.github.com> Co-authored-by: Anne Marie Noronha <noronhaa@mskcc.org> * 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 <noronhaa@mskcc.org> * 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 <noronhaa@mskcc.org> Co-authored-by: anoronh4 <amnoronha1016@gmail.com> Co-authored-by: anoronh4 <amnoronha1016@gmail.com> Co-authored-by: Anne Marie Noronha <noronhaa@mskcc.org>
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May 15, 2020
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