Code

Sentieon DNAseq flow#1044

Code

Merged

maxulysse merged 226 commits intodevnf-core/sarek:devfrom sentieonnf-core/sarek:sentieonCopy head branch name to clipboardJul 10, 2023

+3,572-1,524

Commits

Commits on Apr 12, 2023

• WIP: Adding the aligner sentieon-bwamem to new subworkflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON

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• Minor adjustments for sentieon bwamem

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• Setting up CI-test of sentieon-bwamem

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• Adding package cryptography to python env

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• Blackened

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• Moving license_message.py

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Commits on Apr 13, 2023

• WIP: Trying to avoid using sentieon-bwaindex

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• Move sentieon/bwamem to aligner-section

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• Update conf/modules/prepare_genome.config

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• Update workflows/sarek.nf

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• Update .github/workflows/pytest-workflow.yml

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• Fixing CI-test for sentieon/bwamem and getting rid of more sentieon/bwaindex stuff

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• Merge pull request #994 from nf-core/add_sentieon_bwamem

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Commits on Apr 19, 2023

• WIP: Adding sentieon-dedup

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Commits on Apr 20, 2023

• Changing cram_sentieon_dedup_no_spark to cram_sentieon_dedup

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Commits on Apr 21, 2023

• Removing CHANNEL_SENTIEON_DEDUP_CREATE_CSV

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Commits on Apr 24, 2023

• Improving join operation on index channels

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• Updating git_sha for sentieon/dedup

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• Merge pull request #1002 from nf-core/sentieon_dedup

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Commits on Apr 25, 2023

• Merge pull request #1005 from nf-core/dev

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Commits on Apr 27, 2023

• WIP: Sentieon-haplotyper vcf-flow working. TO-DO: gvcf, joint-germeline, cleanup and more testing.

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• Merge branch 'dev' into sentieon

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• Merge branch 'sentieon' into sentieon_haplotyper

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• Adding sentieon/dedup

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• Adding sentieon/haplotyper

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• Update pytest-workflow.yml

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• Merge pull request #1008 from nf-core/maxulysse-patch-2

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• Adding skip filter functionality for sentieon-haplotyper

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• Merge branch 'sentieon' into sentieon_haplotyper

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Commits on Apr 28, 2023

• Removing md5sum checks on TsTv.qual-files. Those files have unstable md5sums.

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• Changing option skip_haplotypecaller_filter to skip_haplotyper_filter for Sentieon-Haplotyper

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• haplotypecaller -> haplotyper

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Commits on May 2, 2023

• WIP: joint-germline with Sentieon

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• Removing debug print statement

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• Adding tests for sentieon joint-germline

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• prettier

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• Removing import of unused subworkflow BAM_MERGE_INDEX_SAMTOOLS

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Commits on May 3, 2023

• Adding option sentieon_haplotyper_out_format

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• Removing conversion of sentieon_haplotyper_out_format to value channel

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Commits on May 4, 2023

• Adding check for gvcf-files

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• Setting option sentieon_haplotyper_out_format to gvcf

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• Adding some check for running joint_germline with sentieon_haplotyper

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• Fixing name of output gvcf-files

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Commits on May 7, 2023

• Adding tests for sentieon_haplotyper_skip_filter

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Commits on May 8, 2023

• Removing unstable md5 checks

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• WIP: Setting up subworkflow for Sentieon-based joint-calling-germline

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• Removing exception for Sentieon's haplotyper

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• Adding tests for --sentieon_haplotyper_out_format gvcf

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• Creating csv for gvcf-output from Sentieon haplotyper

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• Clean up

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• Adding pytest for both vcf and gvcf

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• Fixing md5sum

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Commits on May 9, 2023

• WIP: Adding Sentieon's Genotyper for joint-germline genotyping

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• prettier

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Commits on May 10, 2023

• Renamed the channel genotype_intervals to genotype_intervals_and_crams

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• Renamed the channel genotype_intervals to genotype_intervals_and_crams

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Commits on May 17, 2023

• Merge branch 'dev' into sentieon_haplotyper

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• Merge branch 'dev' into sentieon

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Commits on May 19, 2023

• Adding the sentieon functions varcal and applyvarcal as local modules

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• Merge branch 'sentieon' into sentieon_haplotyper

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Commits on May 20, 2023

• Changing container nfcore/sentieon:202112.06 to docker.io/nfcore/sentieon:202112.06

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• Merge branch 'sentieon_haplotyper' of https://github.com/nf-core/sarek into sentieon_haplotyper

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• Removing comment

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Commits on May 24, 2023

• Change local Sentieon gvcftyper module to nf-core version

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• nf-core version of nf-module with Sentieons gvcftyper

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• Replacing local sentieon varcal module with nf-core version

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• removing comment

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• Removing argument dict from call to SENTIEON_VARCAL

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• Merge branch 'sentieon_haplotyper' of https://github.com/nf-core/sarek into sentieon_haplotyper

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• Replacing local version of Sentieons applyvarcal module with nf-core version

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Commits on May 25, 2023

• Updating Sentieon modules from nf-core

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• Remove local version of applyvarcal

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• Skipping singularity-based test for CI-test concatenate_vcfs

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• Update nextflow_schema.json

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• Undoing deletion

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• cleaner

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• Renaming ch genotype_intervals_and_crams back to genotype_intervals

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• section for sentieon_joint_germline

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Commits on May 26, 2023

• Undoing the removal of samtools/convert/main.nf from markduplicates section

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• Changing tag joint_germline to sention_joint_germline

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• Update subworkflows/local/bam_variant_calling_haplotypecaller/main.nf

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• Fix typo

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• Merge branch 'sentieon_haplotyper' of https://github.com/nf-core/sarek into sentieon_haplotyper

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• Merge pull request #1007 from nf-core/sentieon_haplotyper

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• merging from dev and fixing conflicts

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• Update .github/workflows/pytest-workflow.yml

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• Update .github/workflows/pytest-workflow.yml

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• Update subworkflows/local/bam_joint_calling_germline_sentieon/main.nf

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• Solving conflicts

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• same meta but shorter syntax

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• Update workflows/sarek.nf

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• Update .github/workflows/pytest-workflow.yml

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• Updating tags

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• Merge branch 'sentieon' of https://github.com/nf-core/sarek into sentieon

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• bug fix

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• Update subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf

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• Update subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf

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• Update modules/nf-core/sentieon/haplotyper/main.nf

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Commits on May 30, 2023

• Moving input arguments for call to SENTIEON_HAPLOTYPER

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• Adding possibility to run Sentieon using license file. #1047

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• Improving indentation

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• Avoiding call to INDEX_DEDUPED (SAMTOOLS_INDEX)

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Commits on May 31, 2023

• Unwanted GATK-haplotypecaller config-stuff in in sentieon-haplotyper-config

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• Irrelevant config-stuff as the sentieon-haplotyper subworkflow currently does not produce bam-files

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• Avoiding addition of variant_caller meta-tag in VCF_VARIANT_FILTERING_GATK. (It should instead by added to meta by the calling subworkflow.)

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• Adding variant_caller meta-tag to vcf-input-channel for VCF_VARIANT_FILTERING_GATK call

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• The merge g(vcf) job was not getting called. Removed meta-tag intervals_name from input-channels before calling groupTuple(). Also removed meta from dict in call to VCF_VARIANT_FILTERING_GATK.

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Commits on Jun 1, 2023

• Merge branch 'dev' into sentieon

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• Removing outcommented code

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• Sentieon-Dedup generates no crai when bam output is requested.

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• Just adding variantcaller once

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Commits on Jun 2, 2023

• Only adding meta tag variantcaller once

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Commits on Jun 4, 2023

• Merge branch 'dev' into sentieon

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• GATK4_GENOMICSDBIMPORT currently not used for joint_germline with Sentieon

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• Avoid publishing from BAM_JOINT_CALLING_GERMLINE_SENTIEON:SENTIEON_GVCFTYPER

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Commits on Jun 5, 2023

• Merge pull request #1064 from nf-core/sentieon_avoid_publishing

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• Merge branch 'dev' into sentieon

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• cleanup

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• Trying to make the module more flexible

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• Changing sentieon_haplotyper_out_format to sentieon_haplotyper_emit_mode

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Commits on Jun 6, 2023

• Adding description for the new option sentieon_haplotyper_emit_mode

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• Changing the option sentieon_haplotyper_out_format to sentieon_haplotyper_emit_mode

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• Trying to add more tests for the different emit-modes

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• temp hack to trigger pytests

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• Changing vcf-file-extention back to unfiltered.vcf.gz

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• Updating docs with new input params

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• fixing the suffices of the output files

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Commits on Jun 7, 2023

• Removing non-essential tests as the CI-test sentieon/haplotyper was crashing due to missing disk space on GHA server

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• Merge pull request #1074 from nf-core/sentieon_haplotyper_refactored

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• Updating sentieon-modules from modules-repo

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• Updating warnings

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• Removing comment

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• Merge branch 'dev' into sentieon

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Commits on Jun 11, 2023

• resolving merge conflicts

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• Change profile test to test_cache

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• removing prefix test_ from sentieon-dedup test-config

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• Adding sentieon-dedup test-configs to nextflow.config

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• Change profile test to test_cache for sentieon-bwamem test

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Commits on Jun 12, 2023

• Updating sentieon-modules from nf-core modules-repo

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Commits on Jun 14, 2023

• Related to PR FIX: Refactor prefix definition #1108

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Commits on Jun 15, 2023

• Updating docs/usage.md with Sentieon-related info

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• added sentieon in diagrams

  

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Commits on Jun 16, 2023

• WIP: Adding info about Sentieon in docs/output.md

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• Removing legacy module-imports from BAM_SENTIEON_DEDUP

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Commits on Jun 19, 2023

• Publishing bam from sentieon-bwamem

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• Adding test for publishing bam and cram

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• regular if-statement instead of conditional ternary statement

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Commits on Jun 21, 2023

• Modifications for import and displaying Sentieon-Dedup metrics as custom content in MultiQC report

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• Adding test for Sentieon-Dedup metrics in multiQC-report

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• prettier

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• updating sentieon dedup module

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• Update modules.json

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• Update modules.json

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• Merge pull request #1123 from nf-core/display_sentieon_dedup_metrics_in_multiqc

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• Merge pull request #1120 from nf-core/sentieon_publish_bam

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• Merge branch 'dev' into sentieon

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Commits on Jun 22, 2023

• Replacing the substring with in the names of the dedup-related output-files

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• Update conf/modules/markduplicates.config

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• Merge pull request #1132 from nf-core/rename_published_dedup_files

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Commits on Jun 23, 2023

• Dedup and QualCal

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• Sentieon Haplotyper Sentieon joint_germline etc

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• Merge branch 'sentieon' into sentieon_docs

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• Adding info on Sentieon Dedup reports

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• Fixed typo

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• prettier

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• Adding sentieon-dedup-reports to content table

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Commits on Jun 26, 2023

• Avoid redundant index generation in sentieon flow

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• cleanup

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• Fixing closing tag for detail

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Commits on Jun 27, 2023

• Merge pull request #1135 from nf-core/avoid_generating_redundant_index

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• merging sentieon-branch and resolving conflict in subworkflows/local/bam_sentieon_dedup/main.nf

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• Update docs/output.md

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• Update docs/output.md

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• Remove some brackets

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Commits on Jun 28, 2023

• Merge pull request #1131 from nf-core/sentieon_docs

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• Merge pull request #1111 from nicorap/sentieon

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• fix typo + resize pictures

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• fix typo

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• Merge pull request #1136 from maxulysse/sentieon

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• Update .github/workflows/pytest-workflow.yml

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• Updating changelog

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• Adding Sentieon-Haplotyper to the list of variant-callers

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Commits on Jul 1, 2023

• Adding Sentieon BWA-mem to list of aligners

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• Update subworkflows/local/bam_variant_calling_germline_all/main.nf

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Commits on Jul 2, 2023

• Adding list of Sentieon DNAseq tools to statement on Sentieon-PR 1044

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• Fixing alignment of line

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  8af7486

• Update conf/modules/sentieon_haplotyper.config

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  asp8200

  and

  FriederikeHanssen

  authored
  c78cb48

• Update conf/modules/sentieon_joint_germline.config

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  asp8200

  and

  FriederikeHanssen

  authored
  5783b7f

• Update conf/modules/sentieon_joint_germline.config

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  asp8200

  and

  FriederikeHanssen

  authored
  f2502bb

• Fixing alignment of line

  asp8200

  committed
  7a0cbf8

• Moving comment concerning Sentieon QualCal to usage.md

  asp8200

  committed
  a2aa53b

• fixing link

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  792f41d

• Changing absolute link to relative link

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  committed
  a307f9f

• Update docs/usage.md

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  asp8200

  and

  FriederikeHanssen

  authored
  adac9fc

• Improving comment concerning Sentieon support and Sentieon license

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  committed
  a591db6

• Update docs/usage.md

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  asp8200

  and

  FriederikeHanssen

  authored
  c3559bb

• Update docs/usage.md

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  asp8200

  and

  FriederikeHanssen

  authored
  a4ce0ee

Commits on Jul 3, 2023

• Fixing alignment of lines

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  8395902

• Update subworkflows/local/bam_joint_calling_germline_sentieon/main.nf

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  asp8200

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  FriederikeHanssen

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  5501690

• Update subworkflows/local/bam_joint_calling_germline_sentieon/main.nf

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  asp8200

  and

  FriederikeHanssen

  authored
  09ec10d

Commits on Jul 4, 2023

• Removing comment about missing support of genomicsDB by Sentieon GVCFtyper

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  9dafc3b

• Adding comment about missing support of GenomicsDB in Sentieon-based joint germline variant calling subworkflow

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  0c28825

• Adding Sentieon Haplotyper to list of SNP/Indel germline variant callers

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  cd0f8ca

• Adding BSD 2-Clause license to sentieon script bin/license_message.py. Cosmetic changes in this new version of the script.

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  4b1780d

• Removing comment

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  aedab66

• Publish BAM files from aligner when markduplicates AND sentieon-dedup is skipped

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  43f0407

• Running SENTIEON_BWAMEM with the same options as regular bwamem

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  acd6c40

• Adding sentieon bwa mem in header for section on bwa parameters

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  6b8a393

• Fixing md5sums after changing some sentieon bwa mem parameters

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Commits on Jul 5, 2023

• Merge branch 'dev' into sentieon

  maxulysse

  authored
  d41b4df

Commits on Jul 6, 2023

• Ran black on license_message.py

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• prettier

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  81d72cb

• [automated] Fix linting with Prettier

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  committed
  1b844c1

• Update README.md

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  asp8200

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  maxulysse

  authored
  5e75b9c

• Update README.md

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  and

  maxulysse

  authored
  9ff75c5

• Merge branch 'dev' into sentieon

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  23330b3

Commits on Jul 7, 2023

• Removing option --input=false from pytests

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  committed
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Commits on Jul 10, 2023

• Merge branch 'dev' into sentieon

  maxulysse

  authored
  3531f81