Merge pull request #1752 from FriederikeHanssen/fullsize

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## PR checklist

- [ ] 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).

CHANGELOG.md

@@ -52,6 +52,7 @@ A set of connecting glaciers.
 - [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version
 - [1745](https://github.com/nf-core/sarek/pull/1745) - Fix bug where workflow can hang if the email parameter is set
 - [1746](https://github.com/nf-core/sarek/pull/1746) - Fix Sentieon module inputs
+- [1752](https://github.com/nf-core/sarek/pull/1752) - Add `indexcov` and `lofreq` to full size tests. Amend overview figures.
 
 ### Removed
 

conf/test_full.config

@@ -18,7 +18,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'
 
     // Other params
-    tools       = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
+    tools       = 'ngscheckmate,lofreq,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
     split_fastq = 20000000
     intervals   = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
     wes         = true

conf/test_full_germline.config

@@ -18,6 +18,6 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'
 
     // Other params
-    tools       = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
+    tools       = 'indexcov,strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
     split_fastq = 50000000
 }

docs/usage.md

@@ -1244,7 +1244,7 @@ Currently, Sentieon's version of BQSR, QualCal, is not available in Sarek. Recen
 ## Requested resources for the tools
 
 Resource requests are difficult to generalize and are often dependent on input data size. Currently, the number of cpus and memory requested by default were adapted from tests on 5 ICGC paired whole-genome sequencing samples with approximately 40X and 80X depth.
-For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by either setting `--max_memory` and `-max_cpus` or tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).
+For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).
 
 ## CNV calling with CNVkit
 

docs/usage/variantcalling/sarek.md

@@ -88,11 +88,17 @@ They can also be added to the parameters directive in the config file we just ed
 
 ```groovy
 params {
-    max_cpus                  = 2
-    max_memory                = '6.5GB'
-    max_time                  = '2.h'
     use_annotation_cache_keys = true
 }
+
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.5GB',
+        time: '2.h'
+    ]
+}
+
 ```
 
 The parameter `use_annotation_cache_keys` allows the annotation software to deal with the local paths when the cache is downloaded on the environment.