Add Tiddit

CHANGELOG.md

@@ -12,37 +12,38 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 ### `Added`
 
 - [#2](https://github.com/nf-core/sarek/pull/2) - Create `nf-core/sarek` `environment.yml` file
-- [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#7](https://github.com/nf-core/sarek/pull/7), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add CI for `nf-core/sarek`
+- [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#7](https://github.com/nf-core/sarek/pull/7), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add CI for `nf-core/sarek`
 - [#3](https://github.com/nf-core/sarek/pull/3) - Add preprocessing to `nf-core/sarek`
 - [#4](https://github.com/nf-core/sarek/pull/4) - Add variant calling to `nf-core/sarek` with `HaplotypeCaller`, and single mode `Manta` and `Strelka`
 - [#5](https://github.com/nf-core/sarek/pull/5) - Add variant calling to `nf-core/sarek` with `Manta`, `Strelka`, `Strelka Best Practices`, `MuTecT2`, `FreeBayes`, `ASCAT`, `ControlFREEC`
 - [#6](https://github.com/nf-core/sarek/pull/6) - Add default containers for annotation to `nf-core/sarek`
-- [#7](https://github.com/nf-core/sarek/pull/7) - Add annotation
 - [#7](https://github.com/nf-core/sarek/pull/7) - Add MultiQC
+- [#7](https://github.com/nf-core/sarek/pull/7) - Add annotation
 - [#7](https://github.com/nf-core/sarek/pull/7) - Add social preview image in `png` and `svg` format
 - [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#11](https://github.com/nf-core/sarek/pull/11) - Add helper script `run_tests.sh` to run different tests
 - [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9) - Add automatic build of specific containers for annotation for `GRCh37`, `GRCh38` and `GRCm38` using `CircleCI`
 - [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11) - Add helper script `build_reference.sh` to build small reference from [nf-core/test-datasets:sarek](https://github.com/nf-core/test-datasets/tree/sarek)
 - [#7](https://github.com/nf-core/sarek/pull/7), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add helper script `download_image.sh` to download containers for testing
 - [#8](https://github.com/nf-core/sarek/pull/8) - Add test configation for easier testing
 - [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11) - Add scripts for `ASCAT`
+- [#10](https://github.com/nf-core/sarek/pull/10) - Add `TIDDIT` to detect structural variants
 - [#11](https://github.com/nf-core/sarek/pull/11) - Add automatic build of specific containers for annotation for `CanFam3.1` using `CircleCI`
 - [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add posters and abstracts
-- [#12](https://github.com/nf-core/sarek/pull/12) - Use `label` for processes configation
-- [#12](https://github.com/nf-core/sarek/pull/12) - Add helper scripts `filter_locifile.py` and `selectROI.py`
 - [#12](https://github.com/nf-core/sarek/pull/12) - Add helper script `make_snapshot.sh` to make an archive for usage on a secure cluster
+- [#12](https://github.com/nf-core/sarek/pull/12) - Add helper scripts `filter_locifile.py` and `selectROI.py`
+- [#12](https://github.com/nf-core/sarek/pull/12) - Use `label` for processes configation
 - [#13](https://github.com/nf-core/sarek/pull/13) - Add Citation documentation
 - [#13](https://github.com/nf-core/sarek/pull/13) - Add `BamQC` process
 - [#13](https://github.com/nf-core/sarek/pull/13) - Add `CompressVCFsnpEff` and `CompressVCFvep` processes
 - [#18](https://github.com/nf-core/sarek/pull/18) - Add `--no-reports` option for tests + add snpEff,VEP,merge to MULTIPLE test
-- [#18](https://github.com/nf-core/sarek/pull/18) - Add possibility to download other genome for `sareksnpeff` and `sarekvep` containers
-- [#18](https://github.com/nf-core/sarek/pull/18) - Add params `--skip` to skip specified QC tools
 - [#18](https://github.com/nf-core/sarek/pull/18) - Add logo to MultiQC report
+- [#18](https://github.com/nf-core/sarek/pull/18) - Add params `--skip` to skip specified QC tools
+- [#18](https://github.com/nf-core/sarek/pull/18) - Add possibility to download other genome for `sareksnpeff` and `sarekvep` containers
 - [#20](https://github.com/nf-core/sarek/pull/20) - Add `markdownlint` config file
 
 ### `Changed`
 
-- [#1](https://github.com/nf-core/sarek/pull/1), [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#6](https://github.com/nf-core/sarek/pull/6), [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12), [#18](https://github.com/nf-core/sarek/pull/18), [#20](https://github.com/nf-core/sarek/pull/20) - Update docs
+- [#1](https://github.com/nf-core/sarek/pull/1), [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#6](https://github.com/nf-core/sarek/pull/6), [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12), [#18](https://github.com/nf-core/sarek/pull/18), [#20](https://github.com/nf-core/sarek/pull/20) - Update docs
 - [#4](https://github.com/nf-core/sarek/pull/4) - Update `cancerit-allelecount` from `2.1.2` to `4.0.2`
 - [#4](https://github.com/nf-core/sarek/pull/4) - Update `gatk4` from `4.1.1.0` to `4.1.2.0`
 - [#7](https://github.com/nf-core/sarek/pull/7) - `--sampleDir` is now deprecated, use `--sample` instead

docs/containers.md

@@ -32,6 +32,7 @@ For annotation, the main container can be used, but the cache has to be download
 - Contain **[samtools][samtools-link]** 1.9
 - Contain **[snpEff][snpeff-link]** 4.3.1t
 - Contain **[Strelka2][strelka-link]** 2.9.10
+- Contain **[TIDDIT][tiddit-link]** 2.7.1
 - Contain **[VCFanno][vcfanno-link]** 0.3.1
 - Contain **[VCFtools][vcftools-link]** 0.1.16
 - Contain **[VEP][vep-link]** 96.0
@@ -111,6 +112,7 @@ The `environment.yml` file can easilly be modified if particular versions of too
 [sareksnpeff-docker-badge]: https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg
 [sareksnpeff-docker-link]: https://hub.docker.com/r/nfcore/sareksnpeff
 [strelka-link]: https://github.com/Illumina/strelka
+[tiddit-link]: https://github.com/SciLifeLab/TIDDIT
 [vcfanno-link]: https://github.com/brentp/vcfanno
 [vcftools-link]: https://vcftools.github.io/index.html
 [vep-link]: https://github.com/Ensembl/ensembl-vep

docs/output.md

@@ -24,6 +24,7 @@ The pipeline processes data using the following steps:
         * [`Strelka2`](#Strelka2)
     * Structural variants
         * [`Manta`](#Manta)
+        * [`TIDDIT`](#TIDDIT)
     * Sample heterogeneity, ploidy and CNVs
         * `alleleCounter`
         * [`ConvertAlleleCounts`](#ConvertAlleleCounts)
@@ -48,6 +49,7 @@ The pipeline processes data using the following steps:
         * [`MultiQC`](#MultiQC)
 
 ## Preprocessing
+
 Sarek preprocesses raw FastQ files or unmapped BAM files, based on [GATK best practices](https://software.broadinstitute.org/gatk/best-practices/).
 
 BAM files with Recalibration tables can also be used as an input to start with the recalibration of said BAM files, for more information see [TSV files output information](#TSV-files)
@@ -79,6 +81,7 @@ For all samples:
   * BAM file and index
 
 ### TSV files
+
 The TSV files are autogenerated and can be used by Sarek for further processing and/or variant calling.
 
 For further reading and documentation see the [input documentation](https://github.com/nf-core/sarek/blob/master/docs/input.md).
@@ -89,14 +92,16 @@ For all samples:
 * `duplicateMarked.tsv` and `recalibrated.tsv`
   * TSV files to start Sarek from `recalibration` or `variantcalling` steps.
 * `duplicateMarked_[SAMPLE].tsv` and `recalibrated_[SAMPLE].tsv`
-    * TSV files to start Sarek from `recalibration` or `variantcalling` steps for a specific sample.
+  * TSV files to start Sarek from `recalibration` or `variantcalling` steps for a specific sample.
 
 ## Variant Calling
+
 All the results regarding variant-calling are collected in this directory.
 
 Recalibrated BAM files can also be used as an input to start the Variant Calling, for more information see [TSV files output information](#TSV-files)
 
 ### FreeBayes
+
 [FreeBayes](https://github.com/ekg/freebayes) is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment..
 
 For further reading and documentation see the [FreeBayes manual](https://github.com/ekg/freebayes/blob/master/README.md#user-manual-and-guide).
@@ -108,6 +113,7 @@ For a Tumor/Normal pair only:
   * VCF with Tabix index
 
 ### HaplotypeCaller
+
 [GATK HaplotypeCaller](https://github.com/broadinstitute/gatk) calls germline SNPs and indels via local re-assembly of haplotypes.
 
 Germline calls are provided for all samples, to able comparison of both tumor and normal for possible mixup.
@@ -121,6 +127,7 @@ For all samples:
   * VCF with Tabix index
 
 ### GenotypeGVCFs
+
 [GATK GenotypeGVCFs](https://github.com/broadinstitute/gatk) performs joint genotyping on one or more samples pre-called with HaplotypeCaller.
 
 Germline calls are provided for all samples, to able comparison of both tumor and normal for possible mixup.
@@ -134,6 +141,7 @@ For all samples:
   * VCF with Tabix index
 
 ### MuTect2
+
 [GATK MuTect2](https://github.com/broadinstitute/gatk) calls somatic SNVs and indels via local assembly of haplotypes.
 
 For further reading and documentation see the [MuTect2 manual](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php).
@@ -144,7 +152,33 @@ For a Tumor/Normal pair only:
 * `MuTect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz` and `MuTect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz.tbi`
   * VCF with Tabix index
 
+### TIDDIT
+
+[TIDDIT](https://github.com/SciLifeLab/TIDDIT)identifies intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions.
+
+Germline calls are provided for all samples, to able comparison of both tumor and normal for possible mixup.
+Low quality calls are removed internally, to simplify processing of variant calls but they are saved by Sarek.
+
+For further reading and documentation see the [TIDDIT manual](https://github.com/SciLifeLab/TIDDIT/blob/master/README.md).
+
+For all samples:
+**Output directory: `results/VariantCalling/[SAMPLE]/TIDDIT`**
+
+* `TIDDIT_[SAMPLE].vcf.gz` and `TIDDIT_[SAMPLE].vcf.gz.tbi`
+  * VCF with Tabix index
+* `TIDDIT_[SAMPLE].signals.tab`
+  * tab file describing coverage across the genome, binned per 50 bp
+* `TIDDIT_[SAMPLE].ploidy.tab`
+  * tab file describing the estimated ploïdy and coverage across each contig
+* `TIDDIT_[SAMPLE].old.vcf`
+  * VCF including the low qualiy calls
+* `TIDDIT_[SAMPLE].wig`
+  * wiggle file containing coverage across the genome, binned per 50 bp
+* `TIDDIT_[SAMPLE].gc.wig`
+  * wiggle file containing fraction of gc content, binned per 50 bp
+
 ### Strelka2
+
 [Strelka2](https://github.com/Illumina/strelka) is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
 
 For further reading and documentation see the [Strelka2 user guide](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md).
@@ -167,15 +201,17 @@ For a Tumor/Normal pair:
 
 Using [Strelka Best Practices](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic-configuration-example) with the `candidateSmallIndels` from `Manta`:
 **Output directory: `results/VariantCalling/[TUMOR_vs_NORMAL]/Strelka`**
+
 * `StrelkaBP_[TUMORSAMPLE]_vs_[NORMALSAMPLE]_somatic_indels.vcf.gz` and `StrelkaBP_[TUMORSAMPLE]_vs_[NORMALSAMPLE]_somatic_indels.vcf.gz.tbi`
   * VCF with Tabix index
 * `StrelkaBP_[TUMORSAMPLE]_vs_[NORMALSAMPLE]_somatic_snvs.vcf.gz` and `StrelkaBP_[TUMORSAMPLE]_vs_[NORMALSAMPLE]_somatic_snvs.vcf.gz.tbi`
   * VCF with Tabix index
 
 ### Manta
+
 [Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
 It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
-`Manta` provides a candidate list for small indels also that can be fed to `Strelka` following [Strelka Best Practices](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic-configuration-example.
+`Manta` provides a candidate list for small indels also that can be fed to `Strelka` following [Strelka Best Practices](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic-configuration-example).
 
 For further reading and documentation see the [Manta user guide](https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md).
 
@@ -188,10 +224,12 @@ For all samples:
   * VCF with Tabix index
 
 For Normal sample only:
+
 * `Manta_[NORMALSAMPLE].diploidSV.vcf.gz` and `Manta_[NORMALSAMPLE].diploidSV.vcf.gz.tbi`
   * VCF with Tabix index
 
 For a Tumor sample only:
+
 * `Manta_[TUMORSAMPLE].tumorSV.vcf.gz` and `Manta_[TUMORSAMPLE].tumorSV.vcf.gz.tbi`
   * VCF with Tabix index
 
@@ -208,6 +246,7 @@ For a Tumor/Normal pair only:
   * VCF with Tabix index
 
 ### ConvertAlleleCounts
+
 [ConvertAlleleCounts](https://github.com/nf-core/sarek/blob/master/bin/convertAlleleCounts.r) is a R-script for converting output from AlleleCount to BAF and LogR values.
 
 For a Tumor/Normal pair only:

environment.yml

@@ -26,5 +26,6 @@ dependencies:
   - samtools=1.9
   - snpeff=4.3.1t
   - strelka=2.9.10
+  - tiddit=2.7.1
   - vcfanno=0.3.1
   - vcftools=0.1.16