Merge pull request nf-core#637 from MaxUlysse/Docs

maxulysse · web-flow · commit 432661dc39de · 2018-09-10T13:29:01.000+02:00
Update more Docs
diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -18,6 +18,7 @@ This checklist is for our own reference
 6. Commit and push version updates
 7. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
 8. Choose an appropriate codename for the release
-9. Tweet that new version is released
-10. Commit and push. Continue making more awesome :metal:
-11. Have fika :cake:
+9. Update [bio.tools](https://bio.tools/Sarek) with the new release
+10. Tweet that new version is released
+11. Commit and push. Continue making more awesome :metal:
+12. Have fika :cake:
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,17 +19,19 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
 - [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Improve install script
 - [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Simplify tests
-- [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor docs
+- [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629), [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Refactor docs
 - [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor config
 - [#632](https://github.com/SciLifeLab/Sarek/pull/632) - Use 2 threads and 2 cpus FastQC processes
+- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Update tool version gathering
 
 ### `Removed`
 - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template
 - [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Remove old Dockerfiles
+- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Remove old comments
 
 ### `Fixed`
 - [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix VEP tests
-
+- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Fix links in MD files
 ## [2.1.0] - Ruotes - 2018-08-14
 
 ### `Added`
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# [![Sarek](https://raw.githubusercontent.com/SciLifeLab/Sarek/master/docs/images/Sarek_logo.png "Sarek")](http://opensource.scilifelab.se/projects/sarek/)
+# [![Sarek](https://raw.githubusercontent.com/SciLifeLab/Sarek/master/docs/images/Sarek_logo.png "Sarek")](http://sarek.scilifelab.se/)
 
 #### An open-source analysis pipeline to detect germline or somatic variants from whole genome sequencing
 
@@ -21,7 +21,7 @@ Previously known as the Cancer Analysis Workflow (CAW),
 Sarek is a workflow designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required.
 
 It's built using [Nextflow][nextflow-link], a domain specific language for workflow building.
-Software dependencies are handled using [Docker](https://www.docker.com) or [Singularity](http://singularity.lbl.gov) - container technologies that provide excellent reproducibility and ease of use.
+Software dependencies are handled using [Docker](https://www.docker.com) or [Singularity](https://www.sylabs.io/singularity/) - container technologies that provide excellent reproducibility and ease of use.
 Singularity has been designed specifically for high-performance computing environments.
 This means that although Sarek has been primarily designed for use with the Swedish [UPPMAX HPC systems](https://www.uppmax.uu.se), it should be able to run on any system that supports these two tools.
 
diff --git a/annotate.nf b/annotate.nf
@@ -26,9 +26,13 @@ kate: syntax groovy; space-indent on; indent-width 2;
  https://github.com/SciLifeLab/Sarek/README.md
 --------------------------------------------------------------------------------
  Processes overview
- - RunBcftoolsStats - Run BCFTools stats on vcf before annotation
+ - RunBcftoolsStats - Run BCFTools stats on vcf files
+ - RunVcftools - Run VCFTools on vcf files
  - RunSnpeff - Run snpEff for annotation of vcf files
  - RunVEP - Run VEP for annotation of vcf files
+ - CompressVCF - Compress and index vcf files using tabix
+ - GetVersionSnpeff - Get version of tools
+ - GetVersionVEP - Get version of tools
 ================================================================================
 =                           C O N F I G U R A T I O N                          =
 ================================================================================
@@ -89,8 +93,6 @@ vcfNotToAnnotate.close()
 
 // as now have the list of VCFs to annotate, the first step is to annotate with allele frequencies, if there are any
 
-
-
 (vcfForBCFtools, vcfForVCFtools, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(4)
 
 vcfForVep = vcfForVep.map {
@@ -265,7 +267,7 @@ if (params.verbose) vcfCompressedoutput = vcfCompressedoutput.view {
   "Index : ${it[3].fileName}"
 }
 
-process GetVersionSnpEFF {
+process GetVersionSnpeff {
   publishDir directoryMap.version, mode: 'link'
   output: file("v_*.txt")
   when: 'snpeff' in tools || 'merge' in tools
diff --git a/buildReferences.nf b/buildReferences.nf
@@ -26,7 +26,6 @@ kate: syntax groovy; space-indent on; indent-width 2;
  https://github.com/SciLifeLab/Sarek/README.md
 --------------------------------------------------------------------------------
  Processes overview
- - ProcessReference - Download all references if needed
  - DecompressFile - Extract files if needed
  - BuildBWAindexes - Build indexes for BWA
  - BuildReferenceIndex - Build index for FASTA refs
@@ -144,7 +143,7 @@ process BuildReferenceIndex {
 }
 
 if (params.verbose) ch_referenceIndex.view {
-  "Reference index        : ${it.fileName}"
+  "Reference index     : ${it.fileName}"
 }
 
 process BuildSAMToolsIndex {
diff --git a/conf/containers.config b/conf/containers.config
@@ -38,36 +38,9 @@ process {
   withName:GetVersionASCAT {
     container = "${params.repository}/r-base:${params.tag}"
   }
-  withName:GetVersionBamQC {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionBCFtools {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionBWAsamtools {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionFastQC {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionFreeBayes {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionGATK {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionManta {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
   withName:GetVersionSnpeff {
     container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   }
-  withName:GetVersionStrelka {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
-  withName:GetVersionVCFtools {
-    container = "${params.repository}/sarek:${params.tag}"
-  }
   withName:GetVersionVEP {
     container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
   }
diff --git a/conf/singularity-path.config b/conf/singularity-path.config
@@ -43,42 +43,12 @@ process {
   withName:GetVersionASCAT {
     container = "${params.containerPath}/r-base-${params.tag}.img"
   }
-  withName:GetVersionBamQC {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionBCFtools {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionBWAsamtools {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionFastQC {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionFreeBayes {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionGATK {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionManta {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
   withName:GetVersionSnpeff {
     container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   }
-  withName:GetVersionStrelka {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
-  withName:GetVersionVCFtools {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
   withName:GetVersionVEP {
     container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
   }
-  withName:IndelRealigner {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
   withName:MapReads {
     container = "${params.containerPath}/sarek-${params.tag}.img"
   }
@@ -88,9 +58,6 @@ process {
   withName:MergeBams {
     container = "${params.containerPath}/sarek-${params.tag}.img"
   }
-  withName:RealignerTargetCreator {
-    container = "${params.containerPath}/sarek-${params.tag}.img"
-  }
   withName:RecalibrateBam {
     container = "${params.containerPath}/sarek-${params.tag}.img"
   }
diff --git a/conf/uppmax-localhost.config b/conf/uppmax-localhost.config
@@ -62,9 +62,6 @@ process {
     cpus = 16
     memory = {params.totalMemory}
   }
-  withName:IndelRealigner {
-    memory = {params.singleCPUMem * 2 * task.attempt}
-  }
   withName:MapReads {
     cpus = 16
     memory = {params.totalMemory}
@@ -78,10 +75,6 @@ process {
     cpus = 16
     memory = {params.totalMemory}
   }
-  withName:RealignerTargetCreator {
-    cpus = 4
-    memory = {params.singleCPUMem * 4 * task.attempt}
-  }
   withName:RecalibrateBam {
     memory = {params.singleCPUMem * task.attempt}
   }
diff --git a/conf/uppmax-slurm.config b/conf/uppmax-slurm.config
@@ -42,12 +42,6 @@ process {
     queue = 'core'
     time = {params.runTime * task.attempt}
   }
-  withName:IndelRealigner {
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-    queue = 'core'
-    time = {params.runTime * task.attempt}
-  }
   withName:MapReads {
     time = {params.runTime * task.attempt}
   }
@@ -61,9 +55,6 @@ process {
     queue = 'core'
     time = {params.runTime * task.attempt}
   }
-  withName:RealignerTargetCreator {
-    time = {params.runTime * task.attempt}
-  }
   withName:RecalibrateBam {
     cpus = 8
     memory = {params.singleCPUMem * 8 * task.attempt}
diff --git a/docs/CONFIG.md b/docs/CONFIG.md
@@ -12,41 +12,41 @@ The standard ones are designed to work on a Swedish UPPMAX clusters, and can be
 Every configuration file can be modified for your own use.
 If you want you can specify the use of a config file using `-c <config file>`
 
-### [`containers.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/containers.config)
+### [`containers.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/containers.config)
 
 Define Containers for all process.
 Images will be pulled automatically.
 Use in your own profile if needed.
 
-### [`docker.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/docker.config)
+### [`docker.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/docker.config)
 
 Define Docker Containers for all process.
 Images will be pulled automatically.
 Use in your own profile if needed.
 
-### [`genomes.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/genomes.config)
+### [`genomes.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/genomes.config)
 
 Contain path to all references.
 Modify it if you want to change genome version, or the path to your references files.
 
-### [`singularity-path.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/singularity-path.config)
+### [`singularity-path.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/singularity-path.config)
 
 Define path to Singularity Containers for all process.
 To be used when downloading Singularity Containers, like on a secure UPPMAX cluster.
 Images will not be pulled automatically.
 You need to set them up before.
 
-### [`singularity.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/singularity.config)
+### [`singularity.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/singularity.config)
 
 Define Singularity Containers for all process.
 Images will be pulled automatically.
 Use in your own profile if needed.
 
-### [`travis.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/travis.config)
+### [`travis.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/travis.config)
 
 To be used for Travis (2 cpus) or on small computer for testing purpose
 
-### [`uppmax-slurm.config`](https://github.com/SciLifeLab/Sarek/blob/master/configuration/uppmax-slurm.config)
+### [`uppmax-slurm.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/uppmax-slurm.config)
 
 Slurm configuration for a UPPMAX cluster
 Will run the workflow on `/scratch` using the Nextflow [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch) directive
diff --git a/docs/INSTALL.md b/docs/INSTALL.md
@@ -8,7 +8,7 @@ You can use a small reference genome as testing.
 - See the [Install Nextflow documentation](https://www.nextflow.io/docs/latest/getstarted.html#installation)
 - See the [Reference files documentation](REFERENCES.md)
 - See the [Install Docker documentation](https://docs.docker.com/engine/installation/linux/ubuntu/#install-docker)
-- See the [Install Singularity documentation](http://singularity.lbl.gov/install-linux)
+- See the [Install Singularity documentation](https://www.sylabs.io/guides/2.6/user-guide/quick_start.html#installation)
 
 ## Installation
 
@@ -18,7 +18,7 @@ Nextflow will automatically fetch Sarek from GitHub when launched if `SciLifeLab
 
 Sarek use Singularity containers to package all the different tools.
 
-If you plan to use the automatic pull of Singularity images, you can use the [`singularity.config`](../configuration/singularity.config) configuration file. You can also set up the Nextflow environnement variable `NXF_SINGULARITY_CACHEDIR` to choose where to store them.
+If you plan to use the automatic pull of Singularity images, you can use the [`singularity.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/singularity.config) configuration file. You can also set up the Nextflow environnement variable `NXF_SINGULARITY_CACHEDIR` to choose where to store them.
 
 For example
 ```bash
diff --git a/docs/OUTPUT.md b/docs/OUTPUT.md
@@ -99,11 +99,11 @@ Manta provides a candidate list for small indels also that can be fed to Strelka
 [fastqc]: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 [freebayes]: https://github.com/ekg/freebayes
 [GATK-BP]: https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS
-[haplotypecaller]: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php
+[haplotypecaller]: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php
 [genomicvcf]: https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf
 [manta]: https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#structural-variant-predictions
 [multiqc-link]: http://multiqc.info/
-[mutect2]: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php
+[mutect2]: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php
 [ngi-link]: https://ngisweden.scilifelab.se/
 [picard-md]: http://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates
 [polyphen-link]: http://genetics.bwh.harvard.edu/pph2/
@@ -116,5 +116,5 @@ Manta provides a candidate list for small indels also that can be fed to Strelka
 [speedseq]: https://github.com/SciLifeLab/Sarek/blob/master/scripts/speedseq.filter.awk
 [strelka2]: https://github.com/Illumina/strelka
 [vep-link]: http://www.ensembl.org/Tools/VEP
-[VEP-predictions]: https://www.ensembl.org/info/genome/variation/predicted_data.html
+[VEP-predictions]: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html
 [logo]: https://img.shields.io/github/release/SciLifeLab/Sarek.svg
diff --git a/docs/PROCESS.md b/docs/PROCESS.md
@@ -7,29 +7,27 @@ We divide them for the moment into 5 main steps:
 
 - MapReads - Map reads with BWA
 - MergeBams - Merge BAMs if multilane samples
-- MarkDuplicates - Mark Duplicates with Picard
-- RealignerTargetCreator - Create realignment target intervals
-- IndelRealigner - Realign BAMs as T/N pair
+- MarkDuplicates - Mark Duplicates with GATK4
 - CreateRecalibrationTable - Create Recalibration Table with BaseRecalibrator
 - RecalibrateBam - Recalibrate Bam with PrintReads
 
 ## Germline Variant Calling:
 
 - CreateIntervalBeds - Create and sort intervals into bed files
-- RunHaplotypecaller - Run HaplotypeCaller for GermLine Variant Calling (Parallelized processes)
-- RunGenotypeGVCFs - Run HaplotypeCaller for GermLine Variant Calling (Parallelized processes)
-- ConcatVCF - Merge results from HaplotypeCaller
+- RunHaplotypecaller - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
+- RunGenotypeGVCFs - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
+- ConcatVCF - Merge results from paralellized callers
 - RunSingleStrelka - Run Strelka for Germline Variant Calling
 - RunSingleManta - Run Manta for Single Structural Variant Calling
 
 ## Somatic Variant Calling:
 
 - CreateIntervalBeds - Create and sort intervals into bed files
-- RunMutect1 - Run MuTect1 for Variant Calling (Parallelized processes)
 - RunMutect2 - Run MuTect2 for Variant Calling (Parallelized processes)
 - RunFreeBayes - Run FreeBayes for Variant Calling (Parallelized processes)
-- ConcatVCF - Merge results from Freebayes, MuTect1 and MuTect2
+- ConcatVCF - Merge results from paralellized variant callers
 - RunStrelka - Run Strelka for Variant Calling
+- RunStrelkaBP - Run Strelka Best Practices for Variant Calling
 - RunManta - Run Manta for Structural Variant Calling
 - RunSingleManta - Run Manta for Single Structural Variant Calling
 - RunAlleleCount - Run AlleleCount to prepare for ASCAT
@@ -43,8 +41,15 @@ We divide them for the moment into 5 main steps:
 - RunBamQC - Run qualimap BamQC on recalibrated BAM files
 - RunBcftoolsStats - Run BCFTools stats on vcf files
 - RunVcftools - Run VCFTools on vcf files
+- GetVersionAlleleCount - Get version of tools
+- GetVersionASCAT - Get version of tools
+- GetVersionSnpeff - Get version of tools
+- GetVersionVEP - Get version of tools
+- GetVersionAll - Get version of tools
+- RunMultiQC - Run MultiQC on reports
 
 ## Annotation:
 
 - RunSnpeff - Run snpEff for annotation of vcf files
 - RunVEP - Run VEP for annotation of vcf files
+- CompressVCF - Compress and index vcf files using tabix
diff --git a/docs/REFERENCES.md b/docs/REFERENCES.md
@@ -72,20 +72,12 @@ Use `--genome smallGRCh37` to map against a small reference genome based on GRCh
 
 The `buildReferences.nf` script can download and build the files needed for smallGRCh37, or build the references for GRCh37/smallGRCh37.
 
-### `--download`
-
-Only with `--genome smallGRCh37`. If this option is specify, the [`smallRef`](https://github.com/szilvajuhos/smallRef) repository will be automatically downloaded from GitHub. Not to be used on UPPMAX cluster Bianca or on similarly secured clusters where such things are not working/allowed.
-
-```
-nextflow run buildReferences.nf --download --genome smallGRCh37
-```
-
 ### `--refDir`
 
-Use `--refDir <path to smallRef>` to specify where are the files to process.
+Use `--refDir <path to references>` to specify where are the files to process.
 
 ```
-nextflow run buildReferences.nf --refDir <path to smallRef> --genome <genome>
+nextflow run buildReferences.nf --refDir <path to references> --genome <genome>
 ```
 
 ### `--genome`
diff --git a/docs/USAGE.md b/docs/USAGE.md
diff --git a/docs/USE_CASES.md b/docs/USE_CASES.md
diff --git a/germlineVC.nf b/germlineVC.nf
diff --git a/main.nf b/main.nf
diff --git a/runMultiQC.nf b/runMultiQC.nf
diff --git a/somaticVC.nf b/somaticVC.nf

Original file line number	Diff line number	Diff line change
`@@ -26,7 +26,6 @@ kate: syntax groovy; space-indent on; indent-width 2;`
`26`	`26`	`https://github.com/SciLifeLab/Sarek/README.md`
`27`	`27`	`--------------------------------------------------------------------------------`
`28`	`28`	`Processes overview`
`29`		`- - ProcessReference - Download all references if needed`
`30`	`29`	`- DecompressFile - Extract files if needed`
`31`	`30`	`- BuildBWAindexes - Build indexes for BWA`
`32`	`31`	`- BuildReferenceIndex - Build index for FASTA refs`
`@@ -144,7 +143,7 @@ process BuildReferenceIndex {`
`144`	`143`	`}`
`145`	`144`
`146`	`145`	`if (params.verbose) ch_referenceIndex.view {`
`147`		`- "Reference index : ${it.fileName}"`
	`146`	`+ "Reference index : ${it.fileName}"`
`148`	`147`	`}`
`149`	`148`
`150`	`149`	`process BuildSAMToolsIndex {`