nf-core/sarek: Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

dev

Added

#774 - Add logo for Danish National Genome Center

Changed

#762 - Back to dev
#762 - Update deepvariant module
#773 - Sync TEMPLATE with tools 2.6

Fixed

#762 - Polish CHANGELOG + figures
#766 - Align box description in subway map
#768 - Use double quotes to fix import of singularity images for deepvariant module
#770 - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module
#771 - update to new modules syntax

Deprecated

Removed

3.0.2 - Lájtávrre

Lájtávrre is a lake you can see from the Skierfe mountain, formed by the Rapaätno river.

Added

#691 - Enable PROFILE=conda, PROFILE=docker and PROFILE=singularity for pytest
#716 - Add documentation for Azure recommended config vm_size
#752 - Add tracking of all dependencies starting 3.0

Changed

#679 - Back to dev
#685 - Updating the nf-core modules used by Sarek
#691 - To run the same pytest as before locally, use PROFILE=docker
#692 - Use params.tools=strelka in profile test
#696 - Adding check of md5-sums in CI-tests
#719 - Added boxes to subway map
#720 - Sync TEMPLATE with tools 2.5
#723 - Sync TEMPLATE with tools 2.5.1
#726 - Adapt resource requests
#730 - Reduce number of tests
#731 - Run the somatic test as default on -profile test_full, the germline can be tested with -profile test_full_germline
#733 - Add description for params.cf_chrom_len
#734 - nf-core modules update -a
#736 - More extensive CI for default test
#742 - Requiring the Haplotypecaller to be specified as one of the tools for joint germline genotyping
#752 - Code polishing

Fixed

#679 - Fixed typos in subway maps
#681 - Fixed intermediate files published cf #680
#688 - Fixed VEP plugins issue cf #687
#689 - Fixed when clause for non BWA mem building mapping indexes
#704 - Fixed cf_ploidy to string instead of number
#705 - Fix publishing for processes in alignment_to_fastq subworkflow; prevent tabix computation for known_snps when present; publish umi processed files into preprocessing/umi subdirectory
#706 - Fixed vep_version not found error when running --vep_loftee
#724 - Fixed prettier issue
#727 - Allow .list interval files; remove seconds from GRCh38 file to allow --nucleotides_per_second to be used
#728 - Circumvent issue with controlfreec and length file containing regions not in intervals file
#729 - Trailing commas in --tools, --skip_tools and --use_gatk_spark now raise failure cf #722
#741 - Fix prefix for bcftools sort for joint germline variant calling
#743 - Remove profile definitions in profile to avoid issues with Tower
#758 - Fix Zenodo batch
#760 - Fix CHANGELOG dependencies
#761 - Fix font in subway map and workflow image

Deprecated

Removed

#742 - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files
#757 - Remove errorStrategy in conf/modules.config

3.0.1 - Saiva

Saiva is a lake in the Sarek national park, just below the Skierfe mountain.

Fixed

#708 - Fixes mpileup bug. Update nf-core module samtools/mpileup to subset CRAM file by intervals

3.0 - Skierfe

Skierfe is a mountain in the Sarek national park, and the inspiration for the logo.

Added

#388 - Add cram support + read splitting with SeqKit for speedup
#394 - Add DeepVariant
#411 - cram in csv samplesheet
#448 - Allow to skip base quality recalibration with --skip_bqsr
#449 - @FriederikeHanssen is now a CODEOWNERS
#460 - Add posters
#463 - Add dark/light logo versions
#464, #514 - Add DRAGMAP as a possible aligner
#479 - Add more subworkflows
#485 - --skip_qc, --skip_markduplicates and --skip_bqsr is now --skip_tools
#507, #537 - Subway map for building indexes
#512, #531, #537 - Subway map for pipeline
#522 - Add QC for vcf files & MultiQC
#533 - Add param --only_paired_variant_calling to allow skipping of germline variantcalling for paired samples
#536 - Add --step markduplicates to start from duplicate marking, --step prepare_recalibration now ONLY starts at process BaseRecalibrator & adding bam and cram input support for --step markduplicates, prepare_recalibration, recalibrate, and variant_calling
#538 - Add param --seq_platform, default: ILLUMINA
#545 - Add modules and subworkflows for cnvkit tumor_only mode
#540 - Add modules and subworkflows for cnvkit somatic mode
#557 - Add Haplotypecaller single sample mode together with CNNScoreVariants and FilterVariantTranches
#576 - Add modules and subworkflows for cnvkit germline mode
#582 - Added option --vep_out_format for setting the format of the output-file from VEP to json, tab or vcf (default)
#594 - Add parameter --save_output_as_bam to allow output of result files in BAM format
#595 - Added Haplotypecaller joint germline calling
#597 - Added tiddit for tumor variant calling
#600 - Added description for UMI related params in schema
#604, #617 - Added full size tests WGS 30x NA12878
#613 - Added params --dbnsfp_fields to allow configuration of fields for the dbnsfp VEP plugin
#613 - Added params --dbnsfp_consequence to allow configuration of consequence for the dbnsfp VEP plugin
#613 - Added params --vep_version to allow more configuration on the vep container definition
#620 - Added checks for sex information when running a CNV tools
#623 - Additional checks of data in the input sample sheet
#629 - Added checks to catch inconsistency between supplied samples and requested tools
#632 - Added params --snpeff_version to allow more configuration on the snpeff container definition
#632 - Added params --vep_include_fasta to use the fasta file for annotation
#639 - Adding genes-txt-file and summary-html-file to the published output from snpEff
#647 - Update resource requests for preprocessing based on what worked for 5 ICGC matched WGS samples
#652 - Added full size somatic test profile

Changed

#580 - changed the test_full config to real public WXS data. 1 sample WXS germline, 1 Tumor/Normal pair. https://doi.org/10.1038/sdata.2016.25 and https://doi.org/10.1038/s41587-021-00994-5
#383, #528 - Update CHANGELOG
#390 - Update nextflow_schema.json
#408 - Sync TEMPLATE with tools 2.0.1
#416 - Sync TEMPLATE with tools 2.1
#417 - Merge dsl2 and dev branches
#419 - Improve preprocessing
#420, #455, #459, #633 - nf-core modules update --all
#427 - Update DeepVariant
#462 - Update modules and modules.config
#465 - Improve test_data.config
#466, #478, #492, #521 - Move some local modules to nf-core/modules
#466, #485, #492, #494, #515 - Improve preprocessing subworkflows
#474, #475 - Sync TEMPLATE with tools 2.2
#487, #489, #492, #497, #522, #583 - Improve variant calling subworkflows
#498 - Update docs
#501 - Sync TEMPLATE with tools 2.3
#511 - Sync TEMPLATE with tools 2.3.2
#520 - Improve annotation subworkflows
#537 - Update workflow figure
#539 - Update CITATIONS.md
#544 - Mutect2 is no longer compatible with --no_intervals
#551 - Sync TEMPLATE with tools 2.4
#562 - Restart from --step annotate is now also requiring a CSV file
#563 - Updated subway map
#570 - Extract mpileup into its own subworkflow; zip mpileup files
#571 - Including and using GATK4's mergeVcfs
#572 - Adjusted subway map svg for firefox compatibility
#577 - Update RELEASE_CHECKLIST
#578 - Updated module deeptools/bamcoverage
#585 - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
#581 - TIDDIT is updated to 3.1.0
#593 - update ensembl-vep cache version and module
#600 - Remove TODO in awsfulltest
#606 - Updated ASCAT to version 3.0 as module
#608 - Prevent candidate VCFs from getting published in manta
#618 - Update multiqc module
#618 - Update test yml files
#620 - gender is now sex in the samplesheet
#630 - Update citations file
#632 - Update snpEff version to 5.1 and cache up to 105
#632 - Update VEP version to 106.1 and cache up to 106
#618 - Update multiqc module update test yml files
#618 - Update test yml files
#633 - Update BCFTOOLS version to 1.15.1
#644 - Use -Y for bwa-mem(2) and remove -M
#645 - Merge tests/nextflow.config in conf/test.config
#646 - Update nextflow_schema.json to reflect new parameters and functions, removes --annotation_cache, removes --ascat_chromosomes
#649 - Update, simplify and add more files to all test_*.yml files
#651 - Added TIDDIT_SOMATIC subworkflow
#653 - Coherent results subfolder structure between preprocessing, variantcalling and reporting
#659 - Update usage.md docu section on How to run ASCAT with WES
#661 - Add cnvkit reference creation to index subway map
#662 - Add bgzipped and indexed GATKBundle reference files for GATK.GRCh37 and replace germline-resources with GATKBundle one
#663 - Add separate parameters for ASCAT and ControlFREEC back in
#668 - Update annotation documentation
#674 - Default value for splitting is 50000000

Fixed

#234 - Switching to DSL2
#234, #238 - Add modules and sub workflow for building indices
#234, #252, #256, #283, #334 - Update Nextflow 19.10.0 -> 20.11.0-edge
#239 - Restore Sarek ascii art to header
#241, #248, #250, #257, #259 - Add modules and sub workflow for preprocessing
#242, #244, #245, #246, #247, #249, #252, #256, #263, #264, #283, #285, #338 - Refactor dsl2 branch
#257 - Use a params modules config file
#266, #285, #297 - Add modules and sub workflow for variant calling
#333 - Bump Sarek version to 3.0dev
#334 - Sync dsl2 and dev branches
#342 - Update README.md
#386 - Annotation is back
#410, #412, #584 - Update CI tests
#418 - Fix known_sites channels
#432, #457 - Sort before tabix index
#454 - Input is optional (can actually be found automatically by Sarek if previously run)
#463, #468 - Fix nf-core lint
#513, #527 - CNV is back
#529 - Do not save versions.yml files
#524 - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
#549 - Fix unique lanes required for Freebayes: issue #311, replaces meta.clone() with actual copy of map to avoid issues with https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339
#567 - Fix interval name resolving during scatter/gather by moving logic to modules.config causing name to be correctly resolved on process execution; also fixed duplicate naming when variant callers produce multiple vcf files by adding field type to meta map
#585 - Fix Spark usage for GATK4 modules
#587 - Fix issue with VEP extra files
#581 - TIDDIT is back
#590 - Fix empty folders during scatter/gather
#592 - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue #299, #359, #367
#598, #614, #626 - Remove WARNING message for config selector not matching
#599 - Add checks for correct data type for params.step
#599 - Add checks for no empty --tools with --step variant_calling or --step annotate
#600 - Remove nf-core lint warnings
#602 - Fixed bug in alignment_to_fastq and added tests
#609 - Remove unused intervals code, reorganize combined intervals file
#613 - Fixed filenames for dbnsfp and SpliceAI VEP plugin
#615 - Fix ASCAT igenomes file paths
#619 - Fix issue with checking samplesheet content with AWS
#628 - Fix issue with value converting to string before schema validation
#628 - Fix dbsnp check issue with --step annotate
#618 - Fix bcftools/vcftools sample labelling in multiqc report
#618 - Fix issue with tiddit #621
#618 - Fix channel issue with targets.bed in prepare_intervals
#634 - Fix issue with samtools/mosdepth plots in multiqc_report
#641 - Fix issue with duplicate substring in tools and skip_tools
#642 - Only unzip ref files if tool is run, only publish ref files if --save_reference and simplify CNKit logic
#650 - Fix intervals checks
#654 - Allow any step but annotation to start from BAM files
#655 - Fix --intervals false logic & add versioning for local modules
#658 - Fix split fastq names in multiqc-report
#666 - Simplify multiqc config channel input
#668 - Add snpeff_version and vep_version to schema_ignore_params to avoid issue when specifying on command line
#669 - Fix path to files when creating csv files

Dependencies

Dependency	Old version	New version
`ascat`	2.5.2	3.0.0
`bcftools`	1.9	1.15.1
`bwa-mem2`	2.0	2.2.1
`bwa`	0.7.17	unchanged
`cancerit-allelecount`	4.0.2	4.3.0
`cnvkit`	0.9.6	0.9.9
`control-freec`	11.6	unchanged
`deepvariant`	added	1.3.0
`dragmap`	added	1.2.1
`ensembl-vep`	99.2	106.1
`fastp`	added	0.23.2
`fastqc`	0.11.9	unchanged
`fgbio`	1.1.0	2.0.2
`freebayes`	1.3.2	1.3.5
`gatk4`	4.1.7.0	4.2.6.1
`gawk`	added	5.1.0
`genesplicer`	1.0	removed
`htslib`	1.9	removed
`llvm-openmp`	8.0.1	removed
`manta`	1.6.0	unchanged
`markdown`	3.1.1	removed
`mosdepth`	0.3.3	unchanged
`msisensor-pro`	1.1.a	1.2.0
`msisensor`	0.5	removed
`multiqc`	1.8	1.13a
`openjdk`	added	8.0.312
`openmp`	8.0.1	removed
`p7zip`	added	15.09
`pigz`	2.3.4	unchanged
`pygments`	2.5.2	removed
`pymdown-extensions`	6.0	removed
`qualimap`	2.2.2d	removed
`r-ggplot2`	3.3.0	removed
`samblaster`	0.1.24	0.1.26
`samtools`	1.9	1.15.1
`sed`	added	4.7
`snpeff`	4.3.1t	5.1
`strelka`	2.9.10	unchanged
`svdb`	added	2.6.1
`tabix`	added	1.11
`tiddit`	2.7.1	3.1.0
`trim-galore`	0.6.5	removed
`vcfanno`	0.3.2	removed
`vcftools`	0.1.16	unchanged

Deprecated

Removed

#485 - --skip_qc, --skip_markduplicates and --skip_bqsr is now --skip_tools
#538 - --sequencing_center is now --seq_center
#538 - --markdup_java_options has been removed
#539 - --annotate_tools has been removed
#539 - --cadd_cache, --cadd_indels, --cadd_indels_tbi, --cadd_wg_snvs, --cadd_wg_snvs_tbi have been removed
#539 - --genesplicer has been removed
#539 - conf/genomes.config and params.genomes_base have been removed
#562 - Restart from --step annotate from folder is removed. Use a csv file instead
#571 - Removed the local module concat_vcf
#605 - Removed Scatter/gather from GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING, all intervals are processed together
#643 - Removed Sentieon parameters

2.7.2 - Áhkká

Áhkká is one of the massifs just outside of the Sarek National Park.

Fixed

#566 - Fix caching bug affecting a variable number of MapReads jobs due to non-deterministic state of statusMap during caching evaluation

2.7.1 - Pårtejekna

Pårtejekna is one of glaciers of the Pårte Massif.

Added

#353 - Add support for task retries with exit code 247 (exhibited by Picard MarkDuplicates)
#354 - Add tumor only mode for Mutect2 and MSIsensor
#356 - Add --cf_contamination_adjustment params to adjust contamination with Control-FREEC
#372 - Add --cf_contamination params to specify contamination value with Control-FREEC

Changed

#373 - Sync TEMPLATE with tools 1.14
#376 - Better logo on Github dark Mode
#387 - Fix tables for TSV file content

Fixed

#375, #381, #382, #385 - Fix bugs due to TEMPLATE sync from #373
#378 - Fix Spark related issue due to Docker settings in nextflow.config

Deprecated

Removed

#368 - Remove social preview image to use GitHub OpenGraph

2.7 - Pårte

Pårte is one of the main massif in the Sarek National Park.

Added

#145 - Add UMI annotation and consensus functionality to Sarek
#230 - Add ignore_soft_clipped_bases option for GATK Mutect2 #218
#253 - Add UMI CI testing
#262 - Add nextflow_schema.json
#237, #282 - Add --aligner to choose between bwa and bwa-mem2
#294 - Add Troubleshooting section to docs/usage.md
#302, #304 - Add WES and tumor-only mode for Control-FREEC

Changed

#253, #255, #326, #329 - Update docs
#260, #262, #278, #322 - Sync with TEMPLATE updated from nf-core/tools 1.10.2
#262 - Update issue templates to fit the recommended community standards
#278, #322 - Refactor docs
#284 - Update F1000Research publication to version 2
#284 - Update Scilifelab logo
#317 - Update README.md (Add: QBiC + Friederike/Gisela)
#320 - Set MarkDuplicates MAX_RECORDS_IN_RAM to default value

Fixed

#229 - Fix Control-FREEC restart issue #225
#236 - Fix GATK Mutect2 typo issue #227
#271 - Fix ConcatVCF_Mutect2 SIGPIPE issue #268
#272 - Fix annotation --tools merge issue
#279 - Fix issue with --step prepare_recalibration #267
#280 - Use HTML codes instead of < and > in docs
#288 - Fix test_annotation profile
#289 - Random string added to extractFastqFromDir to avoid name collition
#290, #323 - Faster solving of Conda environment
#293 - Fix typo issue when printing infos #292
#309 - Fixed concatenation of many VCF files
#310 - Fix Github Actions not running after November 16, 2020 (deprecated Github Actions API #739
#329 - Simplify Control-FREEC usage
#331 - Replace spread operator by combine to remove Nextflow deprecation warning

Removed

#234 - Removing obsolete script #92
#262 - Removing deprecated params: annotateTools, annotateVCF, cadd_InDels, cadd_InDels_tbi, cadd_WG_SNVs, cadd_WG_SNVs_tbi, maxMultiqcEmailFileSize, noGVCF, noReports, noStrelkaBP, nucleotidesPerSecond, publishDirMode, sample, sampleDir, saveGenomeIndex, skipQC, snpEff_cache, targetBed
#262 - Removing warning message about deprecated and obsolete params
#324 - --no_gatk_spark is now removed, use --use_gatk_spark instead
#324 - --no_gvcf is now removed, use --generate_gvcf instead

2.6.1 - Gådokgaskatjåhkkå

Gådokgaskatjåhkkå is the highest peak in the Piellorieppe massif.

Changed

#208 - Merge changes from the release PR
#208 - Bump version to 3.0dev
#214 - Update GATK from 4.1.6.0 to 4.1.7.0
#219 - Added awsfulltest.yml GitHub Actions workflow
#222 - Bump version to 2.6.1 and minor release
#223 - Apply comments from the release PR

Fixed

#211 - Extend timeout for pushing to DockerHub for VEP containers
#212 - No AWS test on forks
#214 - Fix channels collision between Freebayes and GATK Mutect2 #200
#214 - Fix warning Invalid tag value for CreateIntervalBeds #209
#214 - Fix GATK Mutect2 issue #210
#219 - Updated awstest.yml GitHub actions workflow
#221 - Fix issue with tmp_dir in BaseRecalibrator process

2.6 - Piellorieppe

Piellorieppe is one of the main massif in the Sarek National Park.

Added

#76 - Add GATK Spark possibilities to Sarek
#87 - Add GATK BaseRecalibrator plot to MultiQC report
#115 - Add @szilvajuhos abstract for ESHG2020
#117 - Add Trim Galore possibilities to Sarek
#141 - Add containers for WBcel235
#150, #151, #154 - Add AWS mega test GitHub Actions
#153 - Add CNVkit possibilities to Sarek
#158 - Added ggplot2 version 3.3.0
#163 - Add MSIsensor in tools and container
#164 - Add --no_gatk_spark params and tests
#167 - Add --markdup_java_options documentation
#169 - Add RELEASE_CHECKLIST.md document
#174 - Add variant_calling.md documentation
#175 - Add Sentieon documentation
#176 - Add empty custom genome in genomes.config to allow genomes that are not in AWS iGenomes
#179, #201 - Add FreeBayes germline variant calling
#180 - Now saving Mapped BAMs (and creating TSV) in minimal setting
#182 - Add possibility to run HaplotypeCaller without dbsnp so it can be used to actually generate vcfs to build a set of known sites (cf gatkforums)
#195 - Now creating TSV for duplicates marked BAMs in minimal setting
#195, #202 - Add --save_bam_mapped params to save mapped BAMs
#197 - Add step prepare_recalibration to allow restart from DuplicatesMarked BAMs
#204 - Add step Control-FREEC to allow restart from pileup files
#205 - Add --skip_markduplicates to allow skipping the MarkDuplicates process

Changed

#76 - Use MarkDuplicatesSpark instead of MarkDuplicates
#76 - Use gatk4-spark instead of gatk4 in environment.yml
#80 - Re-bump dev branch
#85 - Use new merged vcf files for known indels to simplify setting up channel
#104 - Update Figure 1
#107 - Switch params to snake_case
#109 - Update publication with F1000Research preprint
#113 - Move social preview image
#120 - Sync TEMPLATE
#121 - Update MultiQC to 1.8
#126, #131 - Update docs
#131 - Use nfcore/base:1.9 as base for containers
#131 - Update Control-FREEC to 11.5
#131 - Update FastQC to 0.11.9
#131 - Update FreeBayes to 1.3.2
#131 - Update Manta to 1.6.0
#131 - Update Qualimap to 2.2.2d
#131 - Update VEP to 99.2
#141 - Update snpEff cache version from 75 to 87 for GRCh37
#141 - Update snpEff cache version from 86 to 92 for GRCh38
#141 - Update VEP databases to 99
#143 - Revert snpEff cache version to 75 for GRCh37
#143 - Revert snpEff cache version to 86 for GRCh38
#152, #158, #164, #174, #194, #198, #204 - Update docs
#164 - Update gatk4-spark from 4.1.4.1 to 4.1.6.0
#180, #195 - Improve minimal setting
#183, #204 - Update input.md documentation
#197 - Output directory DuplicateMarked is now replaced by DuplicatesMarked
#204 - Output directory controlFREEC is now replaced by Control-FREEC

Fixed

#83 - Fix some typos in docs/input.md
#107 - Fix linting
#110 - Fix snpEff report issue cf #106
#126 - Fix iGenomes paths
#127, #128 - Fix ASCAT
#129 - Fix issue with Channel channel ch_software_versions_yaml
#129 - Apply @drpatelh fix for mardown_to_html.py compatibility with Python 2
#129 - Removed Python 3.7.3 from conda environment due to incompatibility
#129 - Change ascii characters that were not supported from the output.md docs
#140 - Fix extra T/N combinations for ASCAT cf #136
#141 - Fix download_cache.nf script to download cache for snpEff and VEP
#143 - Fix annotation CI testing with snpEff and VEP
#144 - Fix CircleCI for building VEP containers
#146 - Fix --no_intervals for GATK Mutect2 cf #135
#156 - Fix typos
#156 - Fix issues with dbsnp files while using only Sention tools
#158 - Fix typo with params.snpeff_cache to decide containers for snpEff
#164 - Fix issues when running with Sentieon
#164 - Add more VCFs to annotation
#167 - Add --markdup_java_options documentation to fix #166
#178 - Fix Sentieon variant calling, now using deduped bam files
#188 - Fix input/output channels for process IndexBamFile to match actual files in the mapped.tsv files
#189 - Fix no_intervals for process HaplotypeCaller (the file just need to actually exists...)
#197 - Fix issue with --step recalibrate
#197 - Fix typo in output directory DuplicateMarked -> DuplicatesMarked

Deprecated

#107 - --annotateTools is now deprecated, use --annotate_tools instead
#107 - --cadd_InDels is now deprecated, use --cadd_indels instead
#107 - --cadd_InDels_tbi is now deprecated, use --cadd_indels_tbi instead
#107 - --cadd_WG_SNVs is now deprecated, use --cadd_wg_snvs instead
#107 - --cadd_WG_SNVs_tbi is now deprecated, use --cadd_wg_snvs_tbi instead
#107 - --maxMultiqcEmailFileSize is now deprecated, use --max_multiqc_email_size instead
#107 - --noGVCF is now deprecated, use --no_gvcf instead
#107 - --noStrelkaBP is now deprecated, use --no_strelka_bp instead
#107 - --nucleotidesPerSecond is now deprecated, use --nucleotides_per_second instead
#107 - --publishDirMode is now deprecated, use --publish_dir_mode instead
#107 - --saveGenomeIndex is now deprecated, use --save_reference instead
#107 - --skipQC is now deprecated, use --skip_qc instead
#107 - --snpEff_cache is now deprecated, use --snpeff_cache instead
#107 - --targetBed is now deprecated, use --target_bed instead

Removed

#107 - --acLociGC is now removed, use --ac_loci_gc instead
#107 - --acLoci is now removed, use --ac_loci instead
#107 - --bwaIndex is now removed, use --bwa instead
#107 - --chrDir is now removed, use --chr_dir instead
#107 - --chrLength is now removed, use --chr_length instead
#107 - --dbsnpIndex is now removed, use --dbsnp_index instead
#107 - --fastaFai is now removed, use --fasta_fai instead
#107 - --genomeDict is now removed, use --dict instead
#107 - --genomeFile is now removed, use --fasta instead
#107 - --genomeIndex is now removed, use --fasta_fai instead
#107 - --germlineResourceIndex is now removed, use --germline_resource_index instead
#107 - --germlineResource is now removed, use --germline_resource instead
#107 - --igenomesIgnore is now removed, use --igenomes_ignore instead
#107 - --knownIndelsIndex is now removed, use --known_indels_index instead
#107 - --knownIndels is now removed, use --known_indels instead
#107 - --singleCPUMem is now removed, use --single_cpu_mem instead
#107 - --snpeffDb is now removed, use --snpeff_db instead
#107 - --vepCacheVersion is now removed, use --vep_cache_version instead
#152 - Removed Jenkinsfile
#169 - Removed omicX from README
#181 - Remove duplicate code in nextflow.config

2.5.2 - Jåkkåtjkaskajekna

Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.

Added

#45 - Include Workflow figure in README.md
#46 - Add location to abstracts
#52 - Add support for mouse data GRCm38
#60 - Add no_intervals params
#60 - Add automatic generation of intervals file with BuildIntervals process
#60 - Add minimal support for minimal genome (only fasta, or fasta + knownIndels)
#60 - Add new processes (IndexBamFile, IndexBamRecal) to deal with optional usage of interval files and minimal genome
#60 - Add tests for minimal genome usage
#60 - Add new minimal genomes (TAIR10, EB2, UMD3.1, bosTau8, WBcel235, ce10, CanFam3.1, canFam3, GRCz10, danRer10, BDGP6, dm6, EquCab2, equCab2, EB1, Galgal4, galGal4, Gm01, hg38, hg19, Mmul_1, mm10, IRGSP-1.0, CHIMP2.1.4, panTro4, Rnor_6.0, rn6, R64-1-1, sacCer3, EF2, Sbi1, Sscrofa10.2, susScr3, AGPv3) to igenomes.config
#61 - Add params split_fastq
#61 - Add test SPLITFASTQ
#66 - Add Sentieon possibilities to Sarek

Changed

#54 - Bump version to 2.5.2dev
#60 - Some process (BaseRecalibrator, ApplyBQSR, Mpileup) have now optional usage of interval files
#60 - Update documentation
#71 - Update README
#71 - Update CHANGELOG
#74 - Update docs
#74 - Improve CI tests (both Jenkins and GitHub actions tests)
#74 - Move all CI from ci-extra.yml to ci.yml

Removed

#46 - Remove mention of old build.nf script which was included in main.nf
#74 - Remove download_image.sh and run_tests.sh scripts
#76 - Remove runOptions = "-u \$(id -u):\$(id -g)" in nextflow.config to enable Spark possibilities

Fixed

#40 - Fix issue with publishDirMode within test profile
#42 - Fix typos, and minor updates in README.md
#43 - Fix automated VEP builds with circleCI
#54 - Apply fixes from release 2.5.1
#58 - Fix issue with .interval_list file from the GATK bundle #56 that was not recognized in the CreateIntervalsBed process
#71 - Fix typos in CHANGELOG
#73 - Fix issue with label memory_max for BaseRecalibrator process #72

2.5.1 - Årjep-Ålkatjjekna

Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.

Added

#53 - Release 2.5.1

Fixed

#48 - Fix singularity.autoMounts issue
#49 - Use correct tag for annotation containers
#50 - Fix paths for scripts

2.5 - Ålkatj

Ålkatj is one of the main massif in the Sarek National Park.

Initial release of nf-core/sarek, created with the nf-core template.

Added

#2 - Create nf-core/sarek environment.yml file
#2, #3, #4, #5, #7, #9, #10, #11, #12 - Add CI for nf-core/sarek
#3 - Add preprocessing to nf-core/sarek
#4 - Add variant calling to nf-core/sarek with HaplotypeCaller, and single mode Manta and Strelka
#5, #34 - Add variant calling to nf-core/sarek with Manta, Strelka, Strelka Best Practices, GATK Mutect2, FreeBayes, ASCAT, ControlFREEC
#6 - Add default containers for annotation to nf-core/sarek
#7 - Add MultiQC
#7 - Add annotation
#7 - Add social preview image in png and svg format
#7, #8, #11, #21 - Add helper script run_tests.sh to run different tests
#7, #8, #9 - Add automatic build of specific containers for annotation for GRCh37, GRCh38 and GRCm38 using CircleCI
#7, #8, #9, #11 - Add helper script build_reference.sh to build small reference from nf-core/test-datasets:sarek
#7, #9, #11, #12 - Add helper script download_image.sh to download containers for testing
#8 - Add test configuration for easier testing
#9, #11 - Add scripts for ASCAT
#10 - Add TIDDIT to detect structural variants
#11 - Add automatic build of specific containers for annotation for CanFam3.1 using CircleCI
#11, #12 - Add posters and abstracts
#12 - Add helper script make_snapshot.sh to make an archive for usage on a secure cluster
#12 - Add helper scripts filter_locifile.py and selectROI.py
#12 - Use label for processes configuration
#13 - Add Citation documentation
#13 - Add BamQC process
#13 - Add CompressVCFsnpEff and CompressVCFvep processes
#18 - Add --no-reports option for tests + add snpEff,VEP,merge to MULTIPLE test
#18 - Add logo to MultiQC report
#18, #29 - Add params --skipQC to skip specified QC tools
#18 - Add possibility to download other genome for sareksnpeff and sarekvep containers
#20 - Add markdownlint config file
#21 - Add tests for latest Nextflow version as well
#21 - Add genomes.config for genomes without AWS iGenomes
#24 - Added GATK4 Mutect2 calling and filtering
#27, #30 - Use Github actions for CI, linting and branch protection
#31 - Add nf-core lint
#31 - Add extra CI to GitHub Actions nf-core extra CI
#35 - Building indexes from nf-core/test-datasets:sarek for CI and small tests

Changed

#1, #2, #3, #4, #5, #6, #7, #8, #9, #10, #11, #12, #18, #20, #21, #23, #29 - Update docs
#4 - Update cancerit-allelecount from 2.1.2 to 4.0.2
#4 - Update gatk4 from 4.1.1.0 to 4.1.2.0
#7, #23 - --sampleDir is now deprecated, use --input instead
#7, #23 - --annotateVCF is now deprecated, use --input instead
#8, #12 - Improve helper script build.nf for downloading and building reference files
#9 - ApplyBQSR is now parallelized
#9 - Fastq files are named following "${idRun}_R1.fastq.gz" in the FastQC output for easier reporting
#9 - Status is now a map with idpatient, idsample as keys (ie: status = statusMap[idPatient, idSample])
#9 - Use ensembl-vep 95.2 instead of 96.0
#11 - Summary HTML from VEP is now in the Reports directory
#12 - Update configuration files
#12 - Disable Docker in singularity profile
#12 - Disable Singularity in docker profile
#12 - Disable Docker and Singularity in conda profile
#12 - Simplify check_max() function
#13 - Merge BamQCmapped and BamQCrecalibrated processes into BamQC process
#13 - Split CompressVCF process into CompressVCFsnpEff and CompressVCFvep processes
#16 - Make scripts in bin/ and scripts/ executable
#18 - Use --no-reports for TravisCI testing
#18 - Add --no-reports for all tests but MULTIPLE in Jenkins
#18, #29 - --noReports is now --skipQC all
#18, #21 - Update logo
#21 - Moved smallGRCh37 path to genomes.config
#23 - Rename genomeFile, genomeIndex and genomeDict by fasta, fastaFai and dict
#23 - --sample is now deprecated, use --input instead
#23 - --genomeFile is now deprecated, use --fasta instead
#23 - --genomeIndex is now deprecated, use --fastaFai instead
#23 - --genomeDict is now deprecated, use --dict instead
#24 - AWS iGenomes config now contains germline resource for GATK4 Mutect2
#30 - Simplify code for MapReads process
#24 - AWS iGenomes config now contains germline resource for GATK4 Mutect2
#31 - Move extra CI to GitHub Actions nf-core extra CI
#32, #33 - Install ASCAT with conda in the environment.yml file
#33 - Use workflow.manifest.version to specify workflow version in path to scripts for ControlFREEC and VEP processes
#35 - Building indexes is now done in main.nf
#35 - build.nf script now only download cache, so renamed to downloadcache.nf
#35 - Use tabix instead of IGVtools to build vcf indexes
#35 - Refactor references handling
#35 - Use Channel values instead of referenceMap
#37 - Bump version for Release
#38 - File names before merge is based on ${idSample}_${idRun} instead of ${idRun}

Removed

#9 - Removed relatedness2 graph from vcftools stats
#13 - Removed BamQCmapped and BamQCrecalibrated processes
#13 - Removed CompressVCF
#18 - Removed params --noReports
#24 - Removed GATK3.X Mutect2
#31 - Remove extra CI from Travis CI and GitHub Actions nf-core CI
#32, #35 - Clean up environment.yml file
#35 - Remove building indexes from build.nf script
#35 - Remove helper script build_reference.sh
#35 - Remove IGVtools
#35 - Remove GATK Mutect2 from MULTIPLE test
#35 - Remove referenceMap and defineReferenceMap() and use Channel values instead

Fixed

#3 - Fix Docker ownership
#11 - Fix MergeMpileup PublishDir
#13 - Fix merge in annotation
#14 - Fix output name for vcf files
#16 - Fix path to Rscript
#18 - Improve cpu usage
#18 - Use same font for nf-core and sarek in ascii art
#20 - Use new logo in README
#20 - Fix path to references genomes
#22 - Fix --singleCPUMem issue
#30 - Fix choice between inputPairReadsFastQC and inputBAMFastQC channels
#31 - Fix badges according to nf-core lint
#31 - Fix rcolorbrewer version according to nf-core lint
#33 - Fix MD Linting
#38 - Avoid collision in MultiQC
#39 - Fix ch_dbsnp channel

Deprecated

#23 - --sample is now deprecated, use --input instead
#23 - --genomeFile is now deprecated, use --fasta instead
#23 - --genomeIndex is now deprecated, use --fastaFai instead
#23 - --genomeDict is now deprecated, use --dict instead
#29 - --noReports is now deprecated, use --skipQC all

2.3.FIX1 - 2019-03-04

Fixed

#742 - Fix output dirs (HaplotypeCaller that was not recognized by annotate.nf introduced by #728)

2.3 - Äpar - 2019-02-27

Äpar is one of the main massif in the Sarek National Park.

Added

#628, #722 - ASCAT now use .gc file
#712, #718 - Added possibilities to run Sarek with conda
#719 - Annotation documentation
#719 - Helper script to download snpeff and VEP cache files
#719 - New --annotation_cache, --snpEff_cache, --vep_cache parameters
#719 - Possibility to use cache wen annotating with snpEff and VEP
#722 - Add path to ASCAT .gc file in igenomes.config
#728 - Update Sarek-data submodule with multiple patients TSV file
#732 - Add cadd_WG_SNVs, cadd_WG_SNVs_tbi, cadd_InDels, cadd_InDels_tbi and cadd_cache params
#732 - Add tabix indexed cache for VEP
#732 - New DownloadCADD process to download CADD files
#732 - Specify values for cadd_WG_SNVs, cadd_WG_SNVs_tbi, cadd_InDels, cadd_InDels_tbi and cadd_cache params in munin.conf file
#732 - Use cadd_cache param for optional use of CADD VEP plugin in annotate.nf
#732 - VEP cache has now fasta files for --HGVS
#735 - Added --exome for Manta, and for StrelkaBP
#735 - Added Travis CI test for targeted

Changed

#710 - Improve release checklist and script
#711 - Improve configuration priorities
#716 - Update paths to containers and AWS iGenomes
#717 - checkFileExtension has changed to hasExtension, and now only verify if file has extension
#717 - fastqFiles renamed to inputFiles
#717 - mapping step can now map BAM files too
#717 - MapReads can now convert BAM to FASTQ and feed it to BWA on the fly
#717, #732 - Update documentation
#719 - snpeff and vep containers are now built with conda
#719 - vepCacheVersion is now defined in conf/genomes.config or conf/igenomes.config
#722 - Add path to ASCAT .gc file in igenomes.config
#722 - Update Sarek-data submodule
#723, #725 - Update docs
#724 - Improved AWS batch configuration
#728 - Improved usage of targetBED params
#728 - Strelka Best Practices output is now prefixed with StrelkaBP_
#728 - VCFs and Annotated VCFs are now ordered by Patient, then tools
#732 - Merge buildContainers.nf and buildReferences.nf in build.nf
#732 - Reduce number of CPUs for RunVEP to 4 cf: VEP docs
#732 - Update VEP from 95.1 to 95.2

Removed

#715 - Remove defReferencesFiles function from buildReferences.nf
#719 - snpEff base container is no longer used
#721 - Remove COSMIC docs
#728 - Remove defineDirectoryMap()
#732 - Remove --database option for VEP cf: VEP docs

Fixed

#720 - bamQC is now run on the recalibrated BAMs, and not after MarkDuplicates
#726 - Fix Ascat ref file input (one file can't be a set)
#727 - bamQC outputs are no longer overwritten (name of dir is now the file instead of sample)
#728 - Fix issue with annotation that was consuming cache channels
#728 - Fix multi sample TSV file #691
#733 - Fix the possibility to specify reference files on the command line

2.2.2 - 2018-12-19

Added

#671 - New publishDirMode param and docs
#673, #675, #676 - Profiles for BinAC and CFC clusters in Tübingen
#679 - Add container for CreateIntervalBeds
#692, #697 - Add AWS iGenomes possibilities (within conf/igenomes.conf)
#694 - Add monochrome and grey logos for light or dark background
#698 - Add btb profile for munin server
#702 - Add font-ttf-dejavu-sans-mono 2.37 and fontconfig 2.1dev to container

Changed

#663 - Update do_release.sh script
#671 - publishDir modes are now params
#677, #698, #703 - Update docs
#678 - Changing VEP to v92 and adjusting CPUs for VEP
#679 - Update old awsbatch configuration
#682 - Specifications for memory and cpus for awsbatch
#693 - Qualimap bamQC is now ran after mapping and after recalibration for better QC
#700 - Update GATK to 4.0.9.0
#702 - Update FastQC to 0.11.8
#705 - Change --TMP_DIR by --tmp-dir for GATK 4.0.9.0 BaseRecalibrator
#706 - Update Travis CI testing

Fixed

#665 - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the MarkDuplicates process, so metrics too
#672 - Process PullSingularityContainers from buildContainers.nf now expect a file with the correct .simg extension for singularity images, and no longer the .img one
#679 - Add publishDirMode for germlineVC.nf
#700 - Fix #699 missing DP in the FORMAT column VCFs for Mutect2
#702 - Fix #701
#705 - Fix #704

2.2.1 - 2018-10-04

Changed

#646 - Update pathfindr submodule
#659 - Update Nextflow to 0.32.0
#660 - Update docs

Fixed

#657 - Fix RunMultiQC.nf bug
#659 - Fix bugs due to updating Nextflow

2.2.0 - Skårki - 2018-09-21

Skårki is one of the main massif in the Sarek National Park.

Added

#613 - Add Issue Templates (bug report and feature request)
#614 - Add PR Template
#615 - Add presentation
#616 - Update documentation
#620 - Add tmp/ to .gitignore
#625 - Add pathfindr as a submodule
#635 - To process targeted sequencing with a target BED
#639 - Add a complete example analysis to docs
#640, #642 - Add helper script for changing version number

Changed

#608 - Update Nextflow required version
#615 - Use splitCsv instead of readlines
#616 - Update CHANGELOG
#621, #638 - Improve install script
#621, #638 - Simplify tests
#627, #629, #637 - Refactor docs
#629 - Refactor config
#632 - Use 2 threads and 2 cpus FastQC processes
#637 - Update tool version gathering
#638 - Use correct .simg extension for Singularity images
#639 - Smaller refactoring of the docs
#640 - Update RELEASE_CHECKLIST
#642 - MultiQC 1.5 -> 1.6
#642 - Qualimap 2.2.2a -> 2.2.2b
#642 - Update conda channel order priorities
#642 - VCFanno 0.2.8 -> 0.3.0
#642 - VCFtools 0.1.15 -> 0.1.16

Removed

#616 - Remove old Issue Template
#629 - Remove old Dockerfiles
#637 - Remove old comments

Fixed

#621 - Fix VEP tests
#637 - Fix links in MD files

2.1.0 - Ruotes - 2018-08-14

Ruotes is one of the main massif in the Sarek National Park.

Added

#555 - snpEff output into VEP
#556 - Strelka Best Practices
#563 - Use SnpEFF reports in MultiQC
#568 - VCFTools process RunVcftools for QC
#574, #580 - Abstracts for NPMI, JOBIM and EACR25
#577 - New repository for testing: Sarek-data
#595 - New library QC for functions bamQC, bcftools, samtoolsStats, vcftools, getVersionBCFtools, getVersionGATK, getVersionManta, getVersionSnpEFF, getVersionStrelka, getVersionVCFtools, getVersionVEP
#595 - New Processes GetVersionBCFtools, GetVersionGATK, GetVersionManta, GetVersionSnpEFF, GetVersionStrelka, GetVersionVCFtools, GetVersionVEP
#595 - New Python script bin/scrape_tool_versions.py inspired by @ewels and @apeltzer
#595 - New QC Process RunVcftools
#596 - New profile for BinAC cluster
#597 - New function sarek_ascii() in SarekUtils
#599, #602 - New Process CompressVCF
#601, #603 - Container for GATK4
#606 - Add test data as a submodule from Sarek-data
#608 - Add documentation on how to install Nextflow on bianca

Changed

#557, #583, #585, #588 - Update help
#560 - GitHub langage for the repository is now Nextflow
#561 - do_all.sh build only containers for one genome reference (default GRCh38) only
#571 - Only one container for all QC tools
#582, #587 - Update figures
#595 - Function defineDirectoryMap() is now part of SarekUtils
#595 - Process GenerateMultiQCconfig replace by function createMultiQCconfig()
#597 - extractBams() now takes an extra parameter
#597 - Move checkFileExtension(), checkParameterExistence(), checkParameterList(), checkReferenceMap(), checkRefExistence(), extractBams(), extractGenders(), returnFile(), returnStatus() and returnTSV() functions to SarekUtils
#597 - Reduce data footprint for Process CreateRecalibrationTable
#597 - Replace deprecated operator phase by join
#599 - Merge is tested with ANNOTATEALL
#604 - Synching GRCh38 wgs_calling_regions bedfiles
#607 - One container approach
#607 - Update to GATK4
#608 - Update Nextflow required version
#616 - Update CHANGELOG
#617 - Replace deprecated Nextflow ``$name syntax with withName

Fixed

#560 - Display message for repository and containerPath
#566 - slurmDownload profile
#579, #584 - Manta output reorganized after modification for Strelka Best Practices process
#585 - Trace file is plain txt
#590, #593 - Fix Singularity installation in Travis CI testing
#598, #601 - Fixes for Python script selectROI.py to work with CLC viewer

Removed

#607 - Remove Mutect1

2.0.0 - 2018-03-23

First release under the Sarek name, from the National Park in Northern Sweden.

Added

Basic wrapper script
Abstract, posters and figures
ROI selector and FreeBayes sanitizer scripts
New logo and icon for the project
Check for existing tumor/normal channel
SarekUtils with checkParams(), checkParameterList(), checkParameterExistence() and isAllowedParams() functions
Some runOptions for docker (prevent some user right problem)
This CHANGELOG

Changed

CAW is now Sarek
Dissect Workflow in 5 new scripts: annotate.nf, main.nf, germlineVC.nf, runMultiQC.nf and somaticVC.nf
report.html, timeline.html and trace.html are generated in Reports/
--version is now used to define the workflow version
Most params are now defined in the base.config file instead of in the scripts
Update RELEASE_CHECKLIST.md
checkParams(), checkParameterList(), checkParameterExistence() and isAllowedParams() in script functions are now called within SarekUtils
nf_required_version is now params.nfRequiredVersion
In buildReferences.nf script, channels now begin by ch_, and files by f_
Use PublishDir mode: 'link' instead of copy
directoryMap now contains params.outDir
#539 - Use Nextflow support of scratch
Reordered Travis CI tests
Update documentation
MultiQC version in container from v1.4 to v1.5
vepgrch37 container base image from release_90.6 to release_92
vepgrch38 container base image from release_90.6 to release_92
VEP version in containers from v90 to v91
nucleotidesPerSecond is now params.nucleotidesPerSecond
Default params.tag is now latest instead of current version, so --tag needs to be specified with the right version to be sure of using the containers corresponding

Deprecated

standard profile
uppmax-localhost.config file

Removed

scripts/skeleton_batch.sh
Old data and tsv files
UPPMAX directories from containers
--step in annotate.nf, germlineVC.nf and somatic.nf
Some runOptions for Singularity (binding not needed anymore on UPPMAX)
download profile

Fixed

#530 - Use $PWD for default outDir
#533 - Replace VEP --pick option by --per_gene

1.2.5 - 2018-01-18

Added

Zenodo for DOI
Delivery README
Document use of the --sampleDir option
Contributing Guidelines
Issue Templates
Release Checklist
--outDir
awsbatch profile
aws-batch.config config file
--noBAMQC params (failing sometimes on Bianca)

Changed

Update Nextflow to 0.26.0 (new fancy report + AWS Batch)
Extra time on Travis CI testing
Replace bundleDir by params.genome_base
Update MultiQC to 1.3 (MEGAQC FTW)
Move and rename some test files

Fixed

Version of COSMIC GRCh37 v83
Write an error message when --sampleDir does not find any FASTQ files
base.config for ConcatVCF process
File specification for recalibrationReport in RecalibrateBam process (got error on AWS Batch)

1.2.4 - 2017-10-27

Fixed

#488 - Better CPU requirements for ConcatVCF
#489 - Exception handling for ASCAT
#490 - CPU requirements for runSingleStrelka and runSingleManta

1.2.3 - 2017-10-18

Fixed

#357 - ASCAT works for GRCh38
#471 - Running Singularity on /scratch
#475 - 16 cpus for local executor
#480 - No tsv file needed for step annotate

1.2.2 - 2017-10-06

Fixed

#479 - Typo in uppmax-localhost.config

1.2.1 - 2017-10-06

Changed

runascat and runconvertallelecounts containers are now replaced by r-base
willmclaren/ensembl-vep:release_90.5 is now base for vepgrch37 and vepgrch38

Removed

vep container
strelka_config.ini file

Fixed

#471 - Running Singularity on /scratch
#472 - Update function to check Nextflow version
#473 - Remove returnMin() function

1.2.0 - 2017-10-02

Changed

Fix version for Manuscript

1.1 - 2017-09-15

Added

Singularity possibilities

Changed

Reports made by default
Intervals file can be a bed file
Normal sample preprocessing + HaplotypeCaller is possible
Better Travis CI tests

Fixed

Memory requirements

1.0 - 2017-02-16

Added

Docker possibilities

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nf-core/sarek: Changelog

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3.0.1 - Saiva

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3.0 - Skierfe

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2.7.2 - Áhkká

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2.7.1 - Pårtejekna

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2.7 - Pårte

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2.6.1 - Gådokgaskatjåhkkå

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2.6 - Piellorieppe

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2.5.2 - Jåkkåtjkaskajekna

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2.5.1 - Årjep-Ålkatjjekna

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2.5 - Ålkatj

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2.3.FIX1 - 2019-03-04

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2.3 - Äpar - 2019-02-27

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2.2.2 - 2018-12-19

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2.2.1 - 2018-10-04

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2.2.0 - Skårki - 2018-09-21

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