Remove Strelka tumor-only somatic variant calling (#1709)

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Closes #803.

I have removed `strelka` **tumor-only somatic variant calling** from the
`bam_variant_calling_tumor_only_all` subworkflow. Also i have updated
the subway image, docs and tests.

Maybe we should leave the PR open for a few days to see if anyone
complains about removing it:
https://nfcore.slack.com/archives/CGFUX04HZ/p1730110553053079

## PR checklist

- [x] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add
tests!
- [ ] If you've added a new tool - have you followed the pipeline
conventions in the [contribution
docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/nf-core/test-datasets)
repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker
--outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run .
-profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and
authors/contributors).

---------

Co-authored-by: fmartinez <[email protected]>

CHANGELOG.md

@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 
 - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
+- [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
 
 ### Dependencies
 

docs/output.md

@@ -554,7 +554,7 @@ In Sentieon's package DNAseq, joint germline variant calling is done by first ru
 For further downstream analysis, take a look [here](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#interpreting-the-germline-multi-sample-variants-vcf).
 
 <details markdown="1">
-<summary>Output files for all single samples (normal or tumor-only)</summary>
+<summary>Output files for single samples (normal)</summary>
 
 **Output directory: `{outdir}/variantcalling/strelka/<sample>/`**
 

docs/usage.md

@@ -559,7 +559,7 @@ Some of the currently, available test profiles:
 | no_intervals    | `nextflow run main.nf -profile test_cache,no_intervals,docker`                        |
 | targeted        | `nextflow run main.nf -profile test_cache,targeted,docker`                            |
 | tools_germline  | `nextflow run main.nf -profile test_cache,tools_germline,docker --tools strelka`      |
-| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools strelka`     |
+| tools_tumoronly | `nextflow run main.nf -profile test_cache,tools_tumoronly,docker --tools mutect2`     |
 | tools_somatic   | `nextflow run main.nf -profile test_cache,tools_somatic,docker --tools strelka`       |
 | trimming        | `nextflow run main.nf -profile test_cache,trim_fastq,docker`                          |
 | umi             | `nextflow run main.nf -profile test_cache,umi,docker`                                 |
@@ -583,7 +583,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |    -    |   x   |    x    |
 | [lofreq](https://github.com/CSB5/lofreq)                                                                |  x  |  x  |   x    |    -    |   x   |    -    |
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
-| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
+| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   -   |    x    |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
 | [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |    -    |   -   |    x    |

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

@@ -6,7 +6,6 @@
 include { BAM_VARIANT_CALLING_CNVKIT                  } from '../bam_variant_calling_cnvkit/main'
 include { BAM_VARIANT_CALLING_FREEBAYES               } from '../bam_variant_calling_freebayes/main'
 include { BAM_VARIANT_CALLING_MPILEUP                 } from '../bam_variant_calling_mpileup/main'
-include { BAM_VARIANT_CALLING_SINGLE_STRELKA          } from '../bam_variant_calling_single_strelka/main'
 include { BAM_VARIANT_CALLING_SINGLE_TIDDIT           } from '../bam_variant_calling_single_tiddit/main'
 include { BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC } from '../bam_variant_calling_tumor_only_controlfreec/main'
 include { BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA        } from '../bam_variant_calling_tumor_only_manta/main'
@@ -46,7 +45,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
     vcf_manta       = Channel.empty()
     vcf_mpileup     = Channel.empty()
     vcf_mutect2     = Channel.empty()
-    vcf_strelka     = Channel.empty()
     vcf_tiddit      = Channel.empty()
     vcf_lofreq      = Channel.empty()
 
@@ -164,20 +162,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA.out.versions)
     }
 
-    // STRELKA
-    if (tools.split(',').contains('strelka')) {
-        BAM_VARIANT_CALLING_SINGLE_STRELKA(
-            cram,
-            dict,
-            fasta.map{ meta, fasta -> [ fasta ] },
-            fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] },
-            intervals_bed_gz_tbi
-        )
-
-        vcf_strelka = BAM_VARIANT_CALLING_SINGLE_STRELKA.out.vcf
-        versions = versions.mix(BAM_VARIANT_CALLING_SINGLE_STRELKA.out.versions)
-    }
-
     // TIDDIT
     if (tools.split(',').contains('tiddit')) {
         BAM_VARIANT_CALLING_SINGLE_TIDDIT(
@@ -195,7 +179,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
         vcf_manta,
         vcf_mutect2,
         vcf_mpileup,
-        vcf_strelka,
         vcf_tiddit
     )
 
@@ -206,7 +189,6 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
     vcf_manta
     vcf_mpileup
     vcf_mutect2
-    vcf_strelka
     vcf_tiddit
 
     versions = versions

tests/config/pytesttags.yml

@@ -389,7 +389,6 @@ strelka:
   - subworkflows/local/bam_variant_calling_single_strelka/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
   - subworkflows/local/bam_variant_calling_somatic_strelka/**
-  - subworkflows/local/bam_variant_calling_tumor_only_all/**
   - tests/csv/3.0/recalibrated_germline.csv
   - tests/csv/3.0/recalibrated_somatic.csv
   - tests/csv/3.0/recalibrated_tumoronly.csv
@@ -408,7 +407,6 @@ strelka_bp:
   - subworkflows/local/bam_variant_calling_somatic_all/**
   - subworkflows/local/bam_variant_calling_somatic_manta/**
   - subworkflows/local/bam_variant_calling_somatic_strelka/**
-  - subworkflows/local/bam_variant_calling_tumor_only_all/**
   - tests/csv/3.0/recalibrated_somatic.csv
   - tests/test_strelka_bp.yml
 
@@ -463,7 +461,6 @@ concatenate_vcfs:
   - subworkflows/local/bam_variant_calling_germline_manta/**
   - subworkflows/local/bam_variant_calling_haplotypecaller/**
   - subworkflows/local/bam_variant_calling_mpileup/**
-  - subworkflows/local/bam_variant_calling_single_strelka/**
   - subworkflows/local/bam_variant_calling_single_tiddit/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
   - subworkflows/local/bam_variant_calling_tumor_only_all/**

tests/test_strelka.yml

@@ -176,80 +176,6 @@
     - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
     - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
     - path: results/reports/samtools/sample1/sample1.recal.cram.stats
-- name: Run variant calling on tumor only sample with strelka
-  command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --outdir results
-  tags:
-    - strelka
-    - tumor_only
-    - variant_calling
-  files:
-    - path: results/csv/variantcalled.csv
-      md5sum: 8d2a5e0ad12781c99e773b828e478d35
-    - path: results/multiqc
-    - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt
-    # conda changes md5sums for test
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary
-      md5sum: fa3112841a4575d104916027c8851b30
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count
-      md5sum: d7f54d09d38af01a574a4930af21cfc9
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual
-      contains: ["19	453	47848	0.00946748	11	50	0.22", "72	458	47880	0.00956558	6	20	0.3", "314	463	47899	0.00966617	1	1	1"]
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/strelka
-      should_exist: false
-    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
-    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
-- name: Run variant calling on tumor only sample with strelka without intervals
-  command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals --outdir results
-  tags:
-    - no_intervals
-    - strelka
-    - tumor_only
-    - variant_calling
-  files:
-    - path: results/csv/variantcalled.csv
-      md5sum: 8d2a5e0ad12781c99e773b828e478d35
-    - path: results/multiqc
-    - path: results/no_intervals.bed
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz.tbi
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt
-    # conda changes md5sums for test
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary
-      md5sum: d1dcce19d82ced016724ace746e95d01
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count
-      md5sum: 9de35bbe9ebe45166b6bd195717f733a
-    - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual
-    # conda changes md5sums for test
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/strelka
-      should_exist: false
-    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
-    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
-    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on somatic sample with strelka
   command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results
   tags:

tests/test_tools_manually.yml

@@ -287,7 +287,7 @@
     - path: results/reports/samtools/sample3/sample3.recal.cram.stats
     # conda changes md5sums for test
 - name: Run full pipeline on tumoronly with most tools
-  command: nextflow run . -profile test --input tests/csv/3.0/fastq_tumor_only.csv --tools cnvkit,freebayes,merge,mpileup,mutect2,snpeff,strelka,tiddit,vep --outdir results
+  command: nextflow run . -profile test --input tests/csv/3.0/fastq_tumor_only.csv --tools cnvkit,freebayes,merge,mpileup,mutect2,snpeff,tiddit,vep --outdir results
   tags:
     - full_pipeline_manual
     - manual