implementation of lofreq

nf-core · Jul 11, 2024 · aeee735 · aeee735
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diff --git a/.prettierrc b/.prettierrc
@@ -0,0 +1 @@
+{}
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -146,6 +146,10 @@
 
   > Danecek P, Auton A, Abecasis G, et al.: The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. PubMed PMID: 21653522; PubMed Central PMCID: PMC3137218.
 
+- [Lofreq](https://pubmed.ncbi.nlm.nih.gov/23066108/)
+
+  >Wilm et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40(22):11189-201.
+
 ## R packages
 
 - [R](https://www.R-project.org/)

diff --git a/README.md b/README.md
@@ -60,6 +60,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `Sentieon Haplotyper`
   - `Strelka2`
   - `TIDDIT`
+  - `Lofreq`
 - Variant filtering and annotation (`SnpEff`, `Ensembl VEP`, `BCFtools annotate`)
 - Summarise and represent QC (`MultiQC`)
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -31,6 +31,7 @@ run_modules:
   - vcftools
   - snpeff
   - vep
+  - lofreq
 
 module_order:
   - fastqc:
@@ -56,6 +57,8 @@ module_order:
       name: "SNPeff"
   - vep:
       name: "VEP"
+  - lofreq:
+      name: "Lofreq"
 
 extra_fn_clean_exts:
   - "_val"

diff --git a/bun.lockb b/bun.lockb
diff --git a/conf/modules/lofreq.config b/conf/modules/lofreq.config
@@ -0,0 +1,31 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+//LOFREQ 
+
+process {
+    executor   = "local"
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } // actualizar códigos de error conforme sea necesario, estos estan tomados de sarek como ejemplo
+    maxRetries = 1
+
+    withName: "LOFREQ_SOMATIC" {
+        publishDir = [
+            mode: params.publishDir_mode,
+            path: { "${params.outdir}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? 'versions.yml' : "${meta.id}/${filename}" }
+            // saveAs: { "${meta.id}/${it}" }
+            // pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+        ext.args = { "--call-indels" }
+    }
+}
diff --git a/conf/modules/lofreq.config:Zone.Identifier b/conf/modules/lofreq.config:Zone.Identifier
@@ -0,0 +1,3 @@
+[ZoneTransfer]
+ZoneId=3
+ReferrerUrl=C:\Users\aito\Desktop\Aitor\Trabajo\Ejemplo Trabajo\nextflow-master.zip
diff --git a/docs/output.md b/docs/output.md
@@ -570,6 +570,13 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
 </details>
 
+#### Lofreq
+
+[Lofreq](https://github.com/CSB5/lofreq) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing, which are usually ignored by other methods or only used for filtering. For further reading and documentation see the [Strelka2 user guide](https://csb5.github.io/lofreq/).
+
+</details>
+
+
 ### Structural Variants
 
 #### Manta

diff --git a/docs/usage.md b/docs/usage.md
@@ -567,6 +567,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [FreeBayes](https://github.com/ekg/freebayes)                                                           |  x  |  x  |   x    |    x    |   x   |    x    |
 | [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) |  x  |  x  |   x    |    x    |   -   |    -    |
 | [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    |   x   |    x    |
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
 | [Strelka2](https://github.com/Illumina/strelka)                                                         |  x  |  x  |   x    |    x    |   x   |    x    |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
@@ -835,8 +836,8 @@ For GATK.GRCh38 the links for each reference file and the corresponding processe
 | dbsnp                 | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
 | dbsnp_tbi             | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
 | dict                  | Baserecalibrator(Spark), CNNScoreVariant, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, MarkDulpicates(Spark), MergeVCFs, Mutect2, Variantrecalibrator                                                                                                                                                                                               | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| fasta                 | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| fasta_fai             | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| fasta                 | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Lofreq, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| fasta_fai             | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Lofreq, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
 | germline_resource     | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                           | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
 | germline_resource_tbi | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                           | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
 | intervals             | ApplyBQSR(Spark), ASCAT, Baserecalibrator(Spark), BCFTools, CNNScoreVariants, ControlFREEC, Deepvariant, FilterVariantTranches, FreeBayes, GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Strelka, mpileup, MSISensorPro, Mutect2, VCFTools                                                                                                                                                                                                      | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |

diff --git a/modules.json b/modules.json
@@ -299,6 +299,11 @@
                         "git_sha": "da4d05d04e65227d4307e87940842f1a14de62c7",
                         "installed_by": ["modules"]
                     },
+                    "lofreq/somatic": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "manta/germline": {
                         "branch": "master",
                         "git_sha": "ebc1733b77c702f19fe42076a5edfcbaa0d84f66",

diff --git a/modules/nf-core/lofreq/somatic/environment.yml b/modules/nf-core/lofreq/somatic/environment.yml
diff --git a/modules/nf-core/lofreq/somatic/main.nf b/modules/nf-core/lofreq/somatic/main.nf
diff --git a/modules/nf-core/lofreq/somatic/meta.yml b/modules/nf-core/lofreq/somatic/meta.yml
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -111,8 +111,8 @@
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for duplicate marking, variant calling and/or for annotation.",
-                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka2\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
-                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Lofreq, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Lofreq, Strelka2\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|lofreq|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",
@@ -356,7 +356,7 @@
                 },
                 "cf_ploidy": {
                     "type": "string",
-                    "default": "2",
+                    "default": 2,
                     "fa_icon": "fas fa-bacon",
                     "help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
                     "description": "Genome ploidy used by ControlFREEC",
@@ -1061,7 +1061,8 @@
                     "fa_icon": "far fa-check-circle",
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode).",
+                    "default": true
                 },
                 "hook_url": {
                     "type": "string",