Absorbs latest nfcore and cgpu; Adds genomeChronicler as tool

[cgpu]

• nf-core bump-version . 2.5.1dev
• Remove PublishDirMode from test profile (Remove PublishDirMode from test profile nf-core/sarek#40)
• update all tools
• minor updates + typo fix
• fix VEP automated builds
• add location for abstracts
• remove reference to old buil.nf script
• update CHANGELOG
• Update docs/reference.md
  Co-Authored-By: Szilveszter Juhos szilveszter.juhos@scilifelab.se
• Update docs/reference.md
• Worfklow (Worfklow nf-core/sarek#45)
• Add workflow figure
• Include workflow figure in readme
• Update CHANGELOG
• add minimal genome and update some processes
• Start adding mouse data
• Update iGenomes.config
• Add tbi
• Drop ASCAT files
• apply changes from 2.5.1 to dev
• bump version to 2.5.2dev
• update CHANGELOG
• update tiddit to 2.8.1
• Use Version 98 of Mouse
• Add for grcm38
• Adjust mus musculus DB
• Annotation
• add smallerGRCh37 and minimalGRCh37
• use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere
• don't use bwa aln
• add automatic generation of intervals file based on fastaFai file
• Adjusted genomes.config
• Should be list
• Set genomes_base to something
• Revert back
• enable CreateIntervalsBed for intervals_list from GATK Bundle
• Add proper calling list
• Use the bed file
• remove temp file
• update CHANGELOG
• Fix genome fa.fai
• Add in mgpv5
• Try short track
• Add in species handling
• Document new parameter species
• Add changelog
• Fix iGenomes stuff
• Add in note about GRCm38
• Fix small fai index issue
• Adjusted quotes in genomes.config
• And the same for igenomes
• Better folder structure for Mouse Genome Project data
• Minor adjustment to propoer paths
• Apply suggestions from code review

Add changes by Maxime
Co-Authored-By: Maxime Garcia max.u.garcia@gmail.com

• Update CHANGELOG.md

Co-Authored-By: Maxime Garcia max.u.garcia@gmail.com

• add minimal tests

• fix processes with no intervals

• add comments

• params noIntervals -> no_intervals

• sort genomes + add news

• code polishing

• update CHANGELOG

• add split_fastq params to split the fastq files with the splitFastq() nf method

• add tests

• temporarely remove TIDDIT tests

• add sention for bwa mem

• disable docker and singularity

• disable container

• add fastaFai for bwamem

• remove module samtools from label sentieon

• fix output from bwa mem

• fix output channel BamMapped from MapReads

• set params.sentieon to null by default

• add SentieonDedup process

• add fastaFai to SentieonDedup process

• fix bam indexing

• add SentieonBQSR

• add label sentieon to SentieonBQSR

• increase cpus for Sentieon BQSR

• remove indexing

• add index for dedup

• bwa mem sentieon specific process

• TSV file for sentieon Dedup

• TSV for every step for Sentieon

• recal -> deduped

• fix input for TSV recalibrate

• enable restart from recalibrate with TSV with Sentieon

• fix sention variant calling from mapping and recalibrate

• code polishing

• add dump tag for imput sample

• add dump tag for bamDedupedSentieon

• code polishing

• remove when statement

• fix typo

• remove tsv for recalibrate with sentieon

• add dnascope dnaseq

• fix dnascope

• add TNscope process

• fix TNscope output

• add pon for TNscope

• add params.pon_index

• add annotation for sention DNAseq, DNAscope, TNscope

• add default pon_index

• typo

• fix typo

• improve automatic annotation

• typo

• typo

• add condition on when statement on TNscope

• clean up

• code polish

• add CODEOWNERS file

• add when statement on all sentieon processes with params.sentieon

• remove munin sentieon specific configs from config

• load sarek specific config

• update path to specific config

• update docs

• remove Freebayes

• update workflow image

• remove old logo

• fix tests

• add docs about params split_fastq

• update CHANGELOG

• improve docs

• more tests but less NF versions

• actually run the tests

• typo

• simplify configs

• add test for mpileup

• go crazy with tests

• fix tests

• includ test.config

• restore FreeBayes

• remove label memory_max from BaseRecalibrator process to fix BaseRecalibrator is eating up all the memory nf-core/sarek#72

• add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests

• update Nextflow version

• add --step annotation to profile

• don't need to specify step here

• move params initalization

• add docs

• fix markdownlint

• more complete docs + sort genomes

• improve tests

• update docs

• update CHANGELOG

• improve script

• fix tests

• better comments

• better comments

• fix error on channel name

• fix output for MergeBamRecal

• fix MergeBamRecal output

• fix TSV file

• update comments and docs

• add warning for sentieon only processes

• nf-core bump-version . 2.5.2

• manual bump-version . 2.5.2

• update workflow image

• downgrade tools for release

• update CHANGELOG

• clean up and update workflow image

• allow a

• fix workflow image

• Apply suggestions from code review

• Apply suggestions from code review

• Update docs/output.md

• Apply suggestions from code review

• Apply suggestions from code review

• Apply suggestions from code review

• Reformats bwa mem | samtools sort command; WIP suboptimal resource usage

• Addresses Modify resources allocated to MapReads #5 ;WIP

• Removes max_ resource alloc labels from MarkDuplicatesSpark

• Replaces .md.bam.bai->.md.bai (same as nf-core)

• Add ${markdup_java_options} to MarkDuplicatesSpark (same as nf-core MarkDuplicates)

• Changes MarkDuplicates --verbosity, DEBUG->INFO

• Changes intervalBed.simpleName->intervalBed.baseName; nf-cored

• Removes label cpus_1 from BaseRecalibratorSpark

• Remove cpus_2 labels from ApplyBQSRSpark; DEBUG->INFO

• Changes pseudo file "no_vepFile.txt" from https to s3 link

• Removes java options from ApplyBQSRSpark

• Removes java options from MarkDupesSpark

• Add java-options to MarkDupesSpark; verbosity INFO->ERROR

• Fixes dupe --java-options; 🤦

• Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp

• Adds soft-coded allocation of resources to MapReads

• Initialise params for MapReads split resource alloc

• Adds neglected curlies around params

• Adds neglected \ to bash vars

• Adds neglected \ to bash vars

• WIP; MapReads optimisations

• Implement resource alloc between bwa and samtools

• Adds max, med soft coded resource alloc

• Re-labels processes (from hard coded resources to soft)

• Adds extra curlies to addrees priority of eval

• Add explicit declaration of maxForks/process

• Update med resource allocation function

• Add echo true and echo of ${bwa_cpus} and ${sort_cpus}

• Hard code heap in MarkDuplicatesSpark at 8g

• Correct expected output bai in MarkDupes

• Removes Spark versions; Not stable with low resources

• Removes sorting; Picard might sort?

• Do not assume sorting in MarkDupes

• Adds explicit --ASSUME_SORT_ORDER unsorted

• Adds missing \

• Omits -k 23

• Bringing sorted back

• Eliminating pipes in mapping step

• Adds bwa -k 23 and GenomeChronicler as tool (Adds bwa -k 23 and GenomeChronicler as tool cgpu/sarek#16)

• Adds -k 23 (bwa mem seed length)
• Exposes as params bwa_cpus, sort_cpus
• Adds GenomeChronicler in tools (sarek logic)

Co-authored-by: Alexander Peltzer apeltzer@users.noreply.github.com
Co-authored-by: Maxime Garcia maxime.garcia@scilifelab.se
Co-authored-by: Szilveszter Juhos szilveszter.juhos@scilifelab.se

Many thanks to contributing to nf-core/sarek!

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• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
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• CHANGELOG.md is updated
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