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.
3.4.0 - Pårtetjåkko
Pårtetjåkko is a mountain in the south of the park.
- #1113 - Adding CNVkit genemetrics module
- #1193 - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline
- #1244 - Add bcf annotate module
- #1252 - Added NGSCheckMate tool for checking that samples come from the same individual
- #1271 - Back to dev
- #1288 - Add nf-test continuous integration (but no tests)
- #1290 - Add nf-test for whole pipeline
- #1278 - Hide sentieon parameters similar to other variant callers
- #1280 - Replacing link to
SentieonDNAscopeModel1.1.model
in Sentieon's S3 with link to same file in igenomes' S3 - #1303 - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin
- #1304 - Update modules
- #1311 - Update local modules with an
environment.yml
file - #1317 - Add new tools to subway map
- #1325 - Move
sentieon_dnascope_model
params intoigenomes.config
- #1325 - Refactor config files
- #1327 - Update modules to have an conda environment name
- #1277 - Fix null value issue for Mutect2 joint calling
- #1287 - Adding label
process_single
to local modules - #1298 - Fix annotation cache usage
- #1301 - Fix nf-prov usage
- #1315 - Avoid clash of configs of
FILTERVARIANTTRANCHES
in the Sentieon-Haplotyper and GATK-Haplotypecaller subworkflows - #1318 - Fix writing of params.json on S3
- #1324 - Fix various typos & code formatting
- #1325 - Update bcfannotate tests and related config files
- #1328 - Fix links to docs in
nextflow_schema.json
anddocs/output.md
- #1328 - Add missing icons in
nextflow_schema.json
- #1330 - Add SnpEff to full sized tests
- #1298 - Remove
--use_annotation_cache_keys
params
Dependency | Old version | New version |
---|---|---|
fastqc | 0.11.9 | 0.12.1 |
multiqc | 1.15 | 1.17 |
script | Old name | New name |
---|---|---|
gatk4spark/applybqsr |
GATK4_APPLYBQSRSPARK |
GATK4SPARK_APPLYBQSR |
gatk4spark/baserecalibrator |
GATK4_BASERECALIBRATORSPARK |
GATK4SPARK_BASERECALIBRATOR |
gatk4spark/markduplicates |
GATK4_MARKDUPLICATESSPARK |
GATK4SPARK_MARKDUPLICATES |
3.3.2 - Ráhpajávvre
Ráhpajávvre is the Lule Sámi spelling of Rapaselet.
- #1248 - Improve annotation-cache docs
- #1261 - Enable cache for annotation generation when using 'merge'
- #1247 - FIX: Result paths for full size test to be correctly displayed on the website
- #1256 - Fix issue with controlfreec container declaration
- #1270 - Revert controlfreec/assesssignificance module to 11.6
Dependency | Old version | New version |
---|---|---|
Control-FREEC/assesssignificance | 11.6b | 11.6 |
3.3.1 - Biellorippjávrre
A lake near the Rapaselet delta.
- #1231 - Back to dev
- #1232 - Fix Zenodo IDs in manifest
- #1236 - Fix annotation cache folder verification when no annotation
- #1240 - Disable JVM Hotspot in all modules/gatk4 (#1030)
- #1241 - Fix axis text of controlfreec plots closing #921
Dependency | Old version | New version |
---|---|---|
Control-FREEC | 11.6 | 11.6b |
3.3.0 - Rapaselet
Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe massif (formerly written Piellorieppe) and the Skårki massif.
- #930 - Add more manual tests
- #1130 - Back to dev
- #1013 - Mutect2 multi sample mode with
--joint_mutect2
- #1153 - Add input validation for Sentieon & FGBio UMI incompatibility
- #1158 - Add preprint
- #1159 - ISMB Poster
- #1173 - CI tests for VQSR track with stub runs
- #1122, #1196 - Add
annotation cache
functionality - #1184 - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR
- #1151 - Refactor codebase
- #1157 - Move all vep args from
ext.args
toparams.vep_custom_args
to allow easier modifications - #1059 - Add
nf-validation
for samplesheet validation - #1160 - Updating tiddit to v3.6.1
- #1166 - More info about
--tools
- #1173 - Refactor single sample filtering of Haplotypecaller generated VCFs (#1053)
- #1174 - Updating multiqc to v1.15
- #1179 - Unhide params
trim_fastq
,umi_read_structure
, andaligner
- #1180 - Updating the nf-core modules
- #1198 - Prepare release
3.3.0
- #1200 - Streamline Github Actions workflows
- #1212 - Use matrix for AWS megatests
- #1218 - Remove Singularity tests for GHA
- #1227 - Update modules
- #1143 -
snpeff_db
is now a string - #1145 - Fixed Zenodo links in
README.md
and inWorkflowMain.groovy
- #1149 - Update
Manta
modules and fix usage of--exome
flag - #1155 - Restore proper rendering in
usage.md
- #1163 - Correcting location of output folder for joint variant calling with GATK's haplotypecaller
- #1169 - Updating Sentieon-modules. (The conda-check in the Sentieon-modules was moved to the script-section. The version of Sentieon remain unchanged.)
- #1171 - Fix channel logic for germline resource to skip GetPileupSummary if not provided
- #1172 - Publish gvcf files when all intervals are processed at once (#764)
- #1173 - Fixed duplicated entries in joint germline recalibrated VCF (#966, #1102), fixed grouping joint germline recalibrated VCF (#1137)
- #1177 - Fix status inference when using nf-validation plugin
- #1181 - Fix join mismatch error in Mutect2 tumor only subworkflow
- #1183 - Add docs for concatentated germline variants
- #1184 - Fix issue with duplicated variants in VCF from Sentieon-based joint-germline variant-calling with VQSR. (Corresponding to #966 for GATK.)
- #1192 - Add
ASCATprofile.png
to ASCAT output docs - #1197 - Improve
tower.yml
file to display reports in Tower (#1190) - #1202 - Remove GHA step that caches Nextflow and bump other out of date actions
- #1203 - Fix issue with Singularity containers on test profiles
- #1204 - Fix issue with nf-validation: lane can be a requirement of bam too now
- #1205 - Less tests triggered
- #1214 - Don't pass in intervals file to ControlFREEC for WGS analysis
- #1215 - Fix
meta.id
for mutect2 tumor_only subworkflows - #1216 - Better test coverage for variant calling
*_all
subworkflows - #1217 - Fix
groupTuple
statement for mutect2 tumor_only subworkflows - #1220 - Fix channel and meta logic for
joint_mutect2
feature - #1221 - Remove
lane
meta field after samplesheet validation to ensure proper merging after mapping - #1222 - Better documentation for annotation cache
- #1224 - Update BCFTOOLS_SORT module with
--temp-dir .
added as option, which was required for Singularity - #1225 - Better test coverage for all tests
- #1227 - Lint warning fix
- #1229 - Fix md5sum for gatk4_spark tests
- #1230 - Fix md5sum for sentieon aligner tests
Dependency | Old version | New version |
---|---|---|
cnvkit |
0.9.9 (samtools 1.16.1) |
0.9.10 (samtools 1.17) |
ensembl-vep |
108 | 110 |
grep |
3.4 | 3.11 |
multiqc |
1.14 | 1.15 |
tiddit |
3.3.2 | 3.6.1 |
3.2.3 - Gällivare
Gällivare is a small lake next to Pierikjaure.
- #1112 - Back to dev
- #1119 - Added
help_text
forinput_output_options
group in schema - #1044 - Adding support for several tools from Sentieon's DNAseq package. The standard fastq-to-vcf processing can now be done using Sentieon's DNAseq tools
ApplyVarCal
,bwa mem
,Dedup
,GVCFtyper
,Haplotyper
,LocusCollector
andVarCal
.
- #1118 - Remove
public_aws_ecr
profile
3.2.2 - Vuoinesluobbalah
Vuoinesluobbalah is a lake close to Bierikjávrre.
- #1087 - Back to dev
- #1087 - Minor modules update
- #1088 - Replace profile
test
bytest_cache
and add atest
profile without hidden files - #1095 - Prepare release
3.2.2
- #1087 - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY #1085
- #1089 - Remove duplicated code
- #1093 - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName.
- #1098 - Fix Channel issue in Mutect2 subworkflow #1094
- #1100 - Remove duplicate index with deepvariant when no_intervals #1069
- #1101 - Remove duplicate index computation for GATK4 Markduplicates & #1065
- #1101 - Fix GATK4 version for GATK4 MarkduplicatesSpark #1068
- #1105 - Remove
params.tracedir
- #1108 - Refactor bad prefix definition for vcf files #938
- #1109 - Fix
mpileup
for variantcalling: onlybcftools
run and file publishing
3.2.1 - Pierikjaure
Pierikjaure is a previous spelling of Bierikjávrre.
- #1078 - Update tabix/bgziptabix module to fix typo
- #1079 - Fixed typo in profile name for tower aws megatests
- #1082 - Patch more modules to use quay.io registry
- #1082 - Update
public_aws_ecr
profile - #1082 - Add quay.io as singularity default registry
3.2.0 - Bierikjávrre
Bierikjávrre is one of the largest lake in Sarek.
- #864 - Added possibilities to export assembled haplotypes and locally realigned reads
- #792 - Added the option
--concatenate_vcfs
for concatenating the germline VCF files. Per default, the resulting vcf-files will be placed under<outDir>/variant_calling/concat
- #889 - Added possibilities to skip variant filtering after Haplotypecaller
- #945 - Adding Adam Talbot to contributor list
- #954 - Adding keys for annotation with snpeff and ensemblvep for
hg19
,hg38
andmm10
- #967 - Adding new
outdir_cache
params - #971 - Subtle bugfix to correct mutation of FASTP output channel objects
- #978 - Validate that patient/sample does not contain spaces
- #981 - Added documentation on generating ASCAT resources for exome and targeted sequencing
- #1041 - Add params
vep_custom_args
to let user specify custom params more easily forVEP
- #1045 - Add
public_aws_ecr
for using ECR hosted containers
- #859 - Back to dev
- #860 - Replace local subworkflow with nf-core version -
vcf_annotate_snpeff
- #865 - Replace local subworkflow with nf-core version -
vcf_annotate_ensemblvep
- #874 - Update all modules
- #882 - Remove exit strategy for
Manta
/Strelka
- #890 - Sync
TEMPLATE
withtools
2.7.1
- #896 - Code refactoring
- #898 - Nextflow minimal version is now
22.10.1
- #898 - Sync
TEMPLATE
withtools
2.7.2
- #909 - Cache test data on GHA
- #928 - No need for BAI when starting from uBAM
- #935 - Add params
build_only_index
to only build index - #936 - Add params
donwload_cache
to download annotation cache - #942 - Update
README.md
- #967 - Update and detail extensively how to use annotation cache
- #968 - Update all modules
- #1011 - Sync
TEMPLATE
withtools
2.8
- #1012 - Better handling of meta maps in
bam_variant_calling_somatic_mutect2
- #1014 -
snpeff_db
is now only thedb
version and notgenome.db
- #1015 - Increase default value for
--nucleotides_per_second
to200000
resulting in 21 groups forGATK.GRCh38
- #1019 - Set a default registry outside of profile scope
- #1031 - Update pipeline summary
- #1032 - Update all modules
- #1051 - Update more modules
- #1056 - Bump pipeline version to
3.2.0
- #870 - Fix output for locally realigned reads from haplotypecaller
- #874 - Remove
CITATION.cff
- #893 - Fix logic of when to execute tabix on dbsnp
- #894 - Add description to
--cnvkit_reference
- #894 - Remove methods description TODO prompt
- #927 - Fix tumor only variant calling issues with freebayes following #896
- #928 - Fix #700
- #929 - Fix somatic variant calling issues with msisensor following #896
- #941 - Fix json validation for
tools
,skip_tools
anduse_gatk_spark
#892 - #954 - Fix missing annotation keys with
snpeff
andensemblvep
forhg19
- #957 - Add
failOnDuplicate
andfailOnMismatch
options to alljoin()
operator where it was possible - #982 - Remove usage of exit statements, using
Nextflow.error
instead - #985 - Cache correctly identifies when it needs to be updated
- #988 - Updated ascat module to fix seed for reproducibility
- #998 - Remove parallelization within a sample for
Manta
- #1014 - Fix calls to
ensemblvep
andsnpeff
containers - #1022 - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.)
- #1039 - Remove concatenate_vcfs tests with singularity, as they are failing due to not enough space on GHA runners
- #1040 - Fix dict channel issue due to #1032
- #1043 - Fix typo in the tags.yml files from #978
- #1048 - Skip tool validation on annotation to fix #949, check that bam is bam and cram is cram #895
- #1050 - Disable GATK VCF filters when joint calling to fix #1025
- #1055 - Fix pattern for fasta file in the json schema
- #1058 - Fix container declaration for VCFTOOLS as it has been updated in the registry
- #1061 - Fix GenomicsDB also works with one interval file, fix results publishing of GenomicsDB
- #1062 - Fix automatic restart from steps
- #1063 - Fix join duplication for manta/strelka
- #898 - Params
enable_conda
was removed - #1070 - Remove Sarek version from workflow and subway map pictures
Dependency | Old version | New version |
---|---|---|
ascat |
3.0.0 | 3.1.1 |
bcftools |
1.15.1 | 1.17 |
deepvariant |
1.4.0 | 1.5.0 |
ensembl-vep |
106.1 | 108.2 |
fastp |
0.23.2 | 0.23.4 |
multiqc |
1.13a | 1.14 |
samtools |
1.16 | 1.17 |
svdb |
2.6.1 | 2.8.1 |
script | Old name | New name |
---|---|---|
ensemblvep/download |
'ENSEMBLVEP_DOWNLOAD' | |
ensemblvep/vep |
'ENSEMBLVEP' | 'ENSEMBLVEP_VEP' |
snpeff/download |
'SNPEFF_DOWNLOAD' | |
snpeff/snpeff |
'SNPEFF' | 'SNPEFF_SNPEFF' |
3.1.2 - Lesser Lule River
Lesser Lule River is English for Lilla Luleälven
- #906 - Remove usages of deprecated
Channel.from
method
3.1.1 - Lilla Luleälven
Lilla Luleälven river's main affluent is Rapaätno.
- #856 - Add annotation for
R64-1-1
andUMD3.1
- #855 - Speed up duplicate marking by using
samtools
for CRAM conversion - #858 - Prepare release
3.1.1
- #851 - Fix
schema
definitionNone
forcf_chrom_len
3.1 - Rapaätno
Rapaätno is the river you can see from the Skierfe mountain.
- #735 - GATK Markduplicates now natively supports CRAM output
- #774 - Add logo for Danish National Genome Center
- #783 - Add paths for chr length used by controlfreec to GRCh38 config
- #820 - Improve documentation on scatter/gather effects
- #833 - Add name to CI tests to avoid confusion between runs
- #735 -
--save_mapped
now saves mapping output in CRAM format - #762 - Back to dev
- #762 - Update deepvariant module
- #773 - Sync
TEMPLATE
withtools
2.6
- #782 - Reduce scatter/gather for full size tests on AWS
- #785 - Update description of
bcftools stats
- #784 - Update all subworkflows names thanks to @scorreard
- #806 - Refactor all tests
- #806 - Split up
modules.config
file - #810 - Update CHANGELOG
- #821 - Change
replace
toputIfAbsent
for automatic search ofinput
if none is provided to avoid overwriting values - #822 - Update modules with
nf-core modules update -a
: Update GATK version to 4.3.0 - #827 - Add
--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader
toGenomicsDB
parameters to speed up the analysis - #842 - Increase default memory for samtools stats
- #844 - All small scale tests are run on PR to
master
- #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
- #777 - Fix mixed up aws full size tests output paths
- #790 - Fix issue #789 somatic mutect2 test
- #793 - Remove DeepVariant GVCF from annotation
- #794 - Fix publishing for unzipped reference files
- #807 - Fix read group when uBAMs are provided (see issue #732)
- #813 - Fix input validation when launching from website (see issue #694)
- #814 - Fix readgroups when using DragMap together with FreeBayes or Mutect2 (see issue #780)
- #817 - Fix CNVKit run on tumor-only sample to be run on all samples
- #828 - Fix issue #763 to run variantcalling when starting form step recalibration
- #837 - Fix Freebayes config selector after subworkflow renaming
- #839 - Remove
copyTo
method that fails on S3 when the source and destination buckets are in different regions - #841 - Fix path priority for
cf_chrom_len
Dependency | Old version | New version |
---|---|---|
bcftools |
1.15.1 | 1.16 |
deepvariant |
1.3.0 | 1.4.0 |
freebayes |
1.3.5 | 1.3.6 |
gatk4 |
4.2.6.1 | 4.3.0.0 |
samtools |
1.15.1 | 1.16.1 |
tiddit |
3.1.0 | 3.3.2 |
3.0.2 - Lájtávrre
Lájtávrre is a lake you can see from the Skierfe mountain, formed by the Rapaätno river.
- #691 - Enable
PROFILE=conda
,PROFILE=docker
andPROFILE=singularity
for pytest - #716 - Add documentation for Azure recommended config vm_size
- #752 - Add tracking of all dependencies starting 3.0
- #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 profiletest
- #696 - Adding check of md5-sums in CI-tests
- #719 - Added boxes to subway map
- #720 - Sync
TEMPLATE
withtools
2.5
- #723 - Sync
TEMPLATE
withtools
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
- #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 forknown_snps
when present; publishumi
processed files intopreprocessing/umi
subdirectory - #706 - Fixed
vep_version
not found error when running--vep_loftee
- #724 - Fixed prettier issue
- #727 - Allow
.list
interval files; removeseconds
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
- #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
inconf/modules.config
3.0.1 - Saiva
Saiva is a lake in the Sarek national park, just below the Skierfe mountain.
- #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.
- #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 processBaseRecalibrator
& addingbam
andcram
input support for--step
markduplicates
,prepare_recalibration
,recalibrate
, andvariant_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 withCNNScoreVariants
andFilterVariantTranches
- #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 tojson
,tab
orvcf
(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 thedbnsfp
VEP
plugin - #613 - Added params
--dbnsfp_consequence
to allow configuration of consequence for thedbnsfp
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
- #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
withtools
2.0.1
- #416 - Sync
TEMPLATE
withtools
2.1
- #417 - Merge
dsl2
anddev
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
withtools
2.2
- #487, #489, #492, #497, #522, #583 - Improve variant calling subworkflows
- #498 - Update docs
- #501 - Sync
TEMPLATE
withtools
2.3
- #511 - Sync
TEMPLATE
withtools
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
withtools
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 to3.1.0
- #593 - update
ensembl-vep
cache version and module - #600 - Remove
TODO
in awsfulltest - #606 - Updated
ASCAT
to version3.0
as module - #608 - Prevent candidate VCFs from getting published in manta
- #618 - Update
multiqc
module - #618 - Update test yml files
- #620 -
gender
is nowsex
in the samplesheet - #630 - Update citations file
- #632 - Update
snpEff
version to5.1
and cache up to105
- #632 - Update
VEP
version to106.1
and cache up to106
- #618 - Update
multiqc
module update test yml files - #618 - Update test yml files
- #633 - Update
BCFTOOLS
version to1.15.1
- #644 - Use
-Y
forbwa-mem(2)
and remove-M
- #645 - Merge
tests/nextflow.config
inconf/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
andControlFREEC
back in - #668 - Update annotation documentation
- #674 - Default value for splitting is
50000000
- #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 to3.0dev
- #334 - Sync
dsl2
anddev
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
tometa
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
andSpliceAI
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
andvep_version
toschema_ignore_params
to avoid issue when specifying on command line - #669 - Fix path to files when creating csv files
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 |
- #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
andparams.genomes_base
have been removed - #562 - Restart from
--step annotate
from folder is removed. Use acsv
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.
- #566 - Fix caching bug affecting a variable number of
MapReads
jobs due to non-deterministic state ofstatusMap
during caching evaluation
2.7.1 - Pårtejekna
Pårtejekna is one of glaciers of the Pårte Massif.
- #353 - Add support for task retries with exit code 247 (exhibited by
Picard MarkDuplicates
) - #354 - Add tumor only mode for
Mutect2
andMSIsensor
- #356 - Add
--cf_contamination_adjustment
params to adjust contamination withControl-FREEC
- #372 - Add
--cf_contamination
params to specify contamination value withControl-FREEC
- #373 - Sync
TEMPLATE
withtools
1.14 - #376 - Better logo on Github dark Mode
- #387 - Fix tables for TSV file content
- #375, #381, #382, #385 - Fix bugs due to
TEMPLATE
sync from #373 - #378 - Fix
Spark
related issue due toDocker
settings innextflow.config
- #368 - Remove social preview image to use GitHub OpenGraph
2.7 - Pårte
Pårte is one of the main massif in the Sarek National Park.
- #145 - Add
UMI annotation and consensus
functionality toSarek
- #230 - Add
ignore_soft_clipped_bases
option forGATK Mutect2
#218 - #253 - Add
UMI
CI
testing - #262 - Add
nextflow_schema.json
- #237, #282 - Add
--aligner
to choose betweenbwa
andbwa-mem2
- #294 - Add
Troubleshooting
section todocs/usage.md
- #302, #304 - Add WES and tumor-only mode for
Control-FREEC
- #253, #255, #326, #329 - Update docs
- #260, #262, #278, #322 - Sync with
TEMPLATE
updated from nf-core/tools1.10.2
- #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
- #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 bycombine
to removeNextflow
deprecation warning
- #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.
- #208 - Merge changes from the release PR
- #208 - Bump version to
3.0dev
- #214 - Update
GATK
from4.1.6.0
to4.1.7.0
- #219 - Added
awsfulltest.yml
GitHub Actions workflow - #222 - Bump version to
2.6.1
and minor release - #223 - Apply comments from the release PR
- #211 - Extend timeout for pushing to DockerHub for VEP containers
- #212 - No AWS test on forks
- #214 - Fix channels collision between
Freebayes
andGATK 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
inBaseRecalibrator
process
2.6 - Piellorieppe
Piellorieppe is one of the main massif in the Sarek National Park.
- #76 - Add
GATK Spark
possibilities to Sarek - #87 - Add
GATK BaseRecalibrator
plot toMultiQC
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
version3.3.0
- #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 ingenomes.config
to allow genomes that are not inAWS 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
withoutdbsnp
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 theMarkDuplicates
process
- #76 - Use
MarkDuplicatesSpark
instead ofMarkDuplicates
- #76 - Use
gatk4-spark
instead ofgatk4
inenvironment.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
to1.8
- #126, #131 - Update docs
- #131 - Use
nfcore/base:1.9
as base for containers - #131 - Update
Control-FREEC
to11.5
- #131 - Update
FastQC
to0.11.9
- #131 - Update
FreeBayes
to1.3.2
- #131 - Update
Manta
to1.6.0
- #131 - Update
Qualimap
to2.2.2d
- #131 - Update
VEP
to99.2
- #141 - Update
snpEff
cache version from75
to87
forGRCh37
- #141 - Update
snpEff
cache version from86
to92
forGRCh38
- #141 - Update
VEP
databases to99
- #143 - Revert
snpEff
cache version to75
forGRCh37
- #143 - Revert
snpEff
cache version to86
forGRCh38
- #152, #158, #164, #174, #194, #198, #204 - Update docs
- #164 - Update
gatk4-spark
from4.1.4.1
to4.1.6.0
- #180, #195 - Improve minimal setting
- #183, #204 - Update
input.md
documentation - #197 - Output directory
DuplicateMarked
is now replaced byDuplicatesMarked
- #204 - Output directory
controlFREEC
is now replaced byControl-FREEC
- #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 forsnpEff
andVEP
- #143 - Fix annotation CI testing with
snpEff
andVEP
- #144 - Fix CircleCI for building
VEP
containers - #146 - Fix
--no_intervals
forGATK Mutect2
cf #135 - #156 - Fix typos
- #156 - Fix issues with
dbsnp
files while using onlySention
tools - #158 - Fix typo with
params.snpeff_cache
to decide containers forsnpEff
- #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 themapped.tsv
files - #189 - Fix
no_intervals
for processHaplotypeCaller
(the file just need to actually exists...) - #197 - Fix issue with
--step recalibrate
- #197 - Fix typo in output directory
DuplicateMarked
->DuplicatesMarked
- #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
- #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.
- #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 withBuildIntervals
process - #60 - Add minimal support for minimal genome (only
fasta
, orfasta
+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
) toigenomes.config
- #61 - Add params
split_fastq
- #61 - Add test
SPLITFASTQ
- #66 - Add
Sentieon
possibilities to Sarek
- #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
toci.yml
- #46 - Remove mention of old
build.nf
script which was included inmain.nf
- #74 - Remove
download_image.sh
andrun_tests.sh
scripts - #76 - Remove
runOptions = "-u \$(id -u):\$(id -g)"
innextflow.config
to enableSpark
possibilities
- #40 - Fix issue with
publishDirMode
withintest
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 theGATK
bundle #56 that was not recognized in theCreateIntervalsBed
process - #71 - Fix typos in
CHANGELOG
- #73 - Fix issue with label
memory_max
forBaseRecalibrator
process #72
2.5.1 - Årjep-Ålkatjjekna
Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.
- #53 - Release
2.5.1
- #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.
- #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
withHaplotypeCaller
, and single modeManta
andStrelka
- #5, #34 - Add variant calling to
nf-core/sarek
withManta
,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
andsvg
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
andGRCm38
usingCircleCI
- #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
usingCircleCI
- #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
andselectROI.py
- #12 - Use
label
for processes configuration - #13 - Add Citation documentation
- #13 - Add
BamQC
process - #13 - Add
CompressVCFsnpEff
andCompressVCFvep
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
andsarekvep
containers - #20 - Add
markdownlint
config file - #21 - Add tests for latest
Nextflow
version as well - #21 - Add
genomes.config
for genomes withoutAWS 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
- #1, #2, #3, #4, #5, #6, #7, #8, #9, #10, #11, #12, #18, #20, #21, #23, #29 - Update docs
- #4 - Update
cancerit-allelecount
from2.1.2
to4.0.2
- #4 - Update
gatk4
from4.1.1.0
to4.1.2.0
- #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 of96.0
- #11 - Summary HTML from
VEP
is now in theReports
directory - #12 - Update configuration files
- #12 - Disable
Docker
insingularity
profile - #12 - Disable
Singularity
indocker
profile - #12 - Disable
Docker
andSingularity
inconda
profile - #12 - Simplify
check_max()
function - #13 - Merge
BamQCmapped
andBamQCrecalibrated
processes intoBamQC
process - #13 - Split
CompressVCF
process intoCompressVCFsnpEff
andCompressVCFvep
processes - #16 - Make scripts in
bin/
andscripts/
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 togenomes.config
- #23 - Rename
genomeFile
,genomeIndex
andgenomeDict
byfasta
,fastaFai
anddict
- #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 forGATK4 Mutect2
- #30 - Simplify code for
MapReads
process - #24 -
AWS iGenomes
config now contains germline resource forGATK4 Mutect2
- #31 - Move extra CI to
GitHub Actions
nf-core extra CI - #32, #33 - Install
ASCAT
withconda
in theenvironment.yml
file - #33 - Use
workflow.manifest.version
to specify workflow version in path to scripts forControlFREEC
andVEP
processes - #35 - Building indexes is now done in
main.nf
- #35 -
build.nf
script now only download cache, so renamed todownloadcache.nf
- #35 - Use
tabix
instead ofIGVtools
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}
- #9 - Removed
relatedness2
graph fromvcftools stats
- #13 - Removed
BamQCmapped
andBamQCrecalibrated
processes - #13 - Removed
CompressVCF
- #18 - Removed params
--noReports
- #24 - Removed
GATK3.X Mutect2
- #31 - Remove extra CI from
Travis CI
andGitHub 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
fromMULTIPLE
test - #35 - Remove
referenceMap
anddefineReferenceMap()
and use Channel values instead
- #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
andsarek
in ascii art - #20 - Use new logo in README
- #20 - Fix path to references genomes
- #22 - Fix
--singleCPUMem
issue - #30 - Fix choice between
inputPairReadsFastQC
andinputBAMFastQC
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
- #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
2.3 - Äpar - 2019-02-27
Äpar is one of the main massif in the Sarek National Park.
- #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
andVEP
cache files - #719 - New
--annotation_cache
,--snpEff_cache
,--vep_cache
parameters - #719 - Possibility to use cache wen annotating with
snpEff
andVEP
- #722 - Add path to ASCAT
.gc
file inigenomes.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
andcadd_cache
params - #732 - Add
tabix
indexed cache forVEP
- #732 - New
DownloadCADD
process to download CADD files - #732 - Specify values for
cadd_WG_SNVs
,cadd_WG_SNVs_tbi
,cadd_InDels
,cadd_InDels_tbi
andcadd_cache
params inmunin.conf
file - #732 - Use
cadd_cache
param for optional use of CADD VEP plugin inannotate.nf
- #732 -
VEP
cache has now fasta files for--HGVS
- #735 - Added
--exome
forManta
, and forStrelkaBP
- #735 - Added
Travis CI
test for targeted
- #710 - Improve release checklist and script
- #711 - Improve configuration priorities
- #716 - Update paths to containers and
AWS iGenomes
- #717 -
checkFileExtension
has changed tohasExtension
, and now only verify if file has extension - #717 -
fastqFiles
renamed toinputFiles
- #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
andvep
containers are now built withconda
- #719 -
vepCacheVersion
is now defined inconf/genomes.config
orconf/igenomes.config
- #722 - Add path to ASCAT
.gc
file inigenomes.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 withStrelkaBP_
- #728 - VCFs and Annotated VCFs are now ordered by Patient, then tools
- #732 - Merge
buildContainers.nf
andbuildReferences.nf
inbuild.nf
- #732 - Reduce number of CPUs for
RunVEP
to4
cf: VEP docs - #732 - Update
VEP
from95.1
to95.2
- #715 - Remove
defReferencesFiles
function frombuildReferences.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
- #720 -
bamQC
is now run on the recalibrated BAMs, and not afterMarkDuplicates
- #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
- #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 (withinconf/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
andfontconfig
2.1dev
to container
- #663 - Update
do_release.sh
script - #671 -
publishDir
modes are now params - #677, #698, #703 - Update docs
- #678 - Changing
VEP
tov92
and adjusting CPUs forVEP
- #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
to4.0.9.0
- #702 - Update
FastQC
to0.11.8
- #705 - Change
--TMP_DIR
by--tmp-dir
forGATK
4.0.9.0
BaseRecalibrator
- #706 - Update
Travis CI
testing
- #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
frombuildContainers.nf
now expect a file with the correct.simg
extension for singularity images, and no longer the.img
one - #679 - Add
publishDirMode
forgermlineVC.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
2.2.0 - Skårki - 2018-09-21
Skårki is one of the main massif in the Sarek National Park.
- #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
- #608 - Update
Nextflow
required version - #615 - Use
splitCsv
instead ofreadlines
- #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
2.1.0 - Ruotes - 2018-08-14
Ruotes is one of the main massif in the Sarek National Park.
- #555 -
snpEff
output intoVEP
- #556 -
Strelka
Best Practices - #563 - Use
SnpEFF
reports inMultiQC
- #568 -
VCFTools
processRunVcftools
for QC - #574, #580 - Abstracts for
NPMI
,JOBIM
andEACR25
- #577 - New repository for testing: Sarek-data
- #595 - New library
QC
for functionsbamQC
,bcftools
,samtoolsStats
,vcftools
,getVersionBCFtools
,getVersionGATK
,getVersionManta
,getVersionSnpEFF
,getVersionStrelka
,getVersionVCFtools
,getVersionVEP
- #595 - New Processes
GetVersionBCFtools
,GetVersionGATK
,GetVersionManta
,GetVersionSnpEFF
,GetVersionStrelka
,GetVersionVCFtools
,GetVersionVEP
- #595 - New
Python
scriptbin/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()
inSarekUtils
- #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
- #557, #583, #585, #588 - Update help
- #560 -
GitHub
langage for the repository is nowNextflow
- #561 -
do_all.sh
build only containers for one genome reference (defaultGRCh38
) only - #571 - Only one container for all QC tools
- #582, #587 - Update figures
- #595 - Function
defineDirectoryMap()
is now part ofSarekUtils
- #595 - Process
GenerateMultiQCconfig
replace by functioncreateMultiQCconfig()
- #597 -
extractBams()
now takes an extra parameter - #597 - Move
checkFileExtension()
,checkParameterExistence()
,checkParameterList()
,checkReferenceMap()
,checkRefExistence()
,extractBams()
,extractGenders()
,returnFile()
,returnStatus()
andreturnTSV()
functions toSarekUtils
- #597 - Reduce data footprint for Process
CreateRecalibrationTable
- #597 - Replace deprecated operator
phase
byjoin
- #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 withwithName
- #560 - Display message for
repository
andcontainerPath
- #566 -
slurmDownload
profile - #579, #584 -
Manta
output reorganized after modification forStrelka Best Practices
process - #585 - Trace file is plain txt
- #590, #593 - Fix
Singularity
installation inTravis CI
testing - #598, #601 - Fixes for
Python
scriptselectROI.py
to work withCLC
viewer
- #607 - Remove
Mutect1
2.0.0 - 2018-03-23
First release under the Sarek
name, from the National Park in Northern Sweden.
- 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
withcheckParams()
,checkParameterList()
,checkParameterExistence()
andisAllowedParams()
functions- Some
runOptions
fordocker
(prevent some user right problem) - This
CHANGELOG
CAW
is nowSarek
- Dissect Workflow in 5 new scripts:
annotate.nf
,main.nf
,germlineVC.nf
,runMultiQC.nf
andsomaticVC.nf
report.html
,timeline.html
andtrace.html
are generated inReports/
--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()
andisAllowedParams()
in script functions are now called withinSarekUtils
nf_required_version
is nowparams.nfRequiredVersion
- In
buildReferences.nf
script, channels now begin bych_
, and files byf_
- Use
PublishDir mode: 'link'
instead ofcopy
directoryMap
now containsparams.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 fromrelease_90.6
torelease_92
vepgrch38
container base image fromrelease_90.6
torelease_92
VEP
version in containers from v90
to v91
nucleotidesPerSecond
is nowparams.nucleotidesPerSecond
- Default
params.tag
is nowlatest
instead of current version, so--tag
needs to be specified with the right version to be sure of using thecontainers
corresponding
standard
profileuppmax-localhost.config
file
scripts/skeleton_batch.sh
- Old data and tsv files
UPPMAX
directories from containers--step
inannotate.nf
,germlineVC.nf
andsomatic.nf
- Some
runOptions
forSingularity
(binding not needed anymore onUPPMAX
) download
profile
1.2.5 - 2018-01-18
Zenodo
for DOI- Delivery README
- Document use of the
--sampleDir
option - Contributing Guidelines
- Issue Templates
- Release Checklist
--outDir
awsbatch
profileaws-batch.config
config file--noBAMQC
params (failing sometimes onBianca
)
- Update
Nextflow
to0.26.0
(new fancy report +AWS Batch
) - Extra time on
Travis CI
testing - Replace
bundleDir
byparams.genome_base
- Update
MultiQC
to1.3
(MEGAQC
FTW) - Move and rename some test files
- Version of
COSMIC
GRCh37
v83
- Write an error message when
--sampleDir
does not find any FASTQ files base.config
forConcatVCF
process- File specification for
recalibrationReport
inRecalibrateBam
process (got error onAWS Batch
)
1.2.4 - 2017-10-27
- #488 - Better CPU requirements for
ConcatVCF
- #489 - Exception handling for
ASCAT
- #490 - CPU requirements for
runSingleStrelka
andrunSingleManta
1.2.3 - 2017-10-18
- #357 -
ASCAT
works forGRCh38
- #471 - Running
Singularity
on/scratch
- #475 - 16 cpus for local executor
- #480 - No
tsv
file needed for stepannotate
1.2.2 - 2017-10-06
- #479 - Typo in
uppmax-localhost.config
1.2.1 - 2017-10-06
runascat
andrunconvertallelecounts
containers are now replaced byr-base
willmclaren/ensembl-vep:release_90.5
is now base forvepgrch37
andvepgrch38
vep
containerstrelka_config.ini
file
- #471 - Running
Singularity
on /scratch - #472 - Update function to check
Nextflow
version - #473 - Remove
returnMin()
function
1.2.0 - 2017-10-02
- Fix version for Manuscript
1.1 - 2017-09-15
Singularity
possibilities
- Reports made by default
- Intervals file can be a bed file
- Normal sample preprocessing +
HaplotypeCaller
is possible - Better
Travis CI
tests
- Memory requirements
1.0 - 2017-02-16
Docker
possibilities