From b11e14935da2573813a7a488020b5937cac52aba Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 18 Mar 2020 14:11:19 +0100
Subject: [PATCH 01/23] small refactor

---
 main.nf | 43 ++++++++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/main.nf b/main.nf
index 788301b250..5ce59d2ace 100644
--- a/main.nf
+++ b/main.nf
@@ -497,11 +497,11 @@ if (params.skip_qc)             summary['QC tools skip']     = skipQC.join(', ')
 
 if (params.trim_fastq) {
     summary['Fastq trim']         = "Fastq trim selected"
-    summary['Trim R1']            = "$params.clip_r1 bp"
-    summary['Trim R2']            = "$params.clip_r2 bp"
-    summary["Trim 3' R1"]         = "$params.three_prime_clip_r1 bp"
-    summary["Trim 3' R2"]         = "$params.three_prime_clip_r2 bp"
-    summary["NextSeq Trim"]       = "$params.trim_nextseq bp"
+    summary['Trim R1']            = "${params.clip_r1} bp"
+    summary['Trim R2']            = "${params.clip_r2} bp"
+    summary["Trim 3' R1"]         = "${params.three_prime_clip_r1} bp"
+    summary["Trim 3' R2"]         = "${params.three_prime_clip_r2} bp"
+    summary["NextSeq Trim"]       = "${params.trim_nextseq} bp"
     summary['Saved Trimmed Fastq'] = params.saveTrimmed ? 'Yes' : 'No'
 }
 
@@ -588,7 +588,7 @@ Channel.from(summary.collect{ [it.key, it.value] })
 
 process Get_software_versions {
     publishDir path:"${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
-        saveAs: { it.indexOf(".csv") > 0 ? it : null }
+        saveAs: {it.indexOf(".csv") > 0 ? it : null}
 
     output:
         file 'software_versions_mqc.yaml' into ch_software_versions_yaml
@@ -986,9 +986,6 @@ fastQCReport = fastQCFQReport.mix(fastQCBAMReport)
 
 fastQCReport = fastQCReport.dump(tag:'FastQC')
 
-outputPairReadsTrimGalore = Channel.create()
-
-if (params.trim_fastq) {
 process TrimGalore {
     label 'TrimGalore'
 
@@ -1009,6 +1006,8 @@ process TrimGalore {
         file("*.{html,zip,txt}") into trimGaloreReport
         set idPatient, idSample, idRun, file("${idSample}_${idRun}_R1_val_1.fq.gz"), file("${idSample}_${idRun}_R2_val_2.fq.gz") into outputPairReadsTrimGalore
 
+    when: params.trim_fastq
+
     script:
     // Calculate number of --cores for TrimGalore based on value of task.cpus
     // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
@@ -1025,22 +1024,30 @@ process TrimGalore {
     tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
     nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
     """
-    trim_galore --cores $cores --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq  ${idSample}_${idRun}_R1.fastq.gz ${idSample}_${idRun}_R2.fastq.gz
+    trim_galore \
+         --cores ${cores} \
+        --paired \
+        --fastqc \
+        --gzip \
+        ${c_r1} ${c_r2} \
+        ${tpc_r1} ${tpc_r2} \
+        ${nextseq} \
+        ${idSample}_${idRun}_R1.fastq.gz ${idSample}_${idRun}_R2.fastq.gz
+
     mv *val_1_fastqc.html "${idSample}_${idRun}_R1.trimmed_fastqc.html"
     mv *val_2_fastqc.html "${idSample}_${idRun}_R2.trimmed_fastqc.html"
     mv *val_1_fastqc.zip "${idSample}_${idRun}_R1.trimmed_fastqc.zip"
     mv *val_2_fastqc.zip "${idSample}_${idRun}_R2.trimmed_fastqc.zip"
     """
-  }
-} else {
-  inputPairReadsTrimGalore
-   .set{outputPairReadsTrimGalore}
-   trimGaloreReport = Channel.empty()
 }
 
+if (!params.trim_fastq) inputPairReadsTrimGalore.close()
+
 // STEP 1: MAPPING READS TO REFERENCE GENOME WITH BWA MEM
 
-inputPairReads = outputPairReadsTrimGalore.mix(inputBam)
+if (params.trim_fastq) inputPairReads = outputPairReadsTrimGalore
+else inputPairReads = inputPairReads.mix(inputBam)
+
 inputPairReads = inputPairReads.dump(tag:'INPUT')
 
 (inputPairReads, inputPairReadsSentieon) = inputPairReads.into(2)
@@ -1062,6 +1069,8 @@ process MapReads {
         set idPatient, idSample, idRun, file("${idSample}_${idRun}.bam") into bamMapped
         set idPatient, val("${idSample}_${idRun}"), file("${idSample}_${idRun}.bam") into bamMappedBamQC
 
+    when: !(params.sentieon)
+
     script:
     // -K is an hidden option, used to fix the number of reads processed by bwa mem
     // Chunk size can affect bwa results, if not specified,
@@ -1211,7 +1220,7 @@ process IndexBamFile {
     output:
         set idPatient, idSample, file(bam), file("*.bai") into indexedBam
 
-    when: !params.known_indels
+    when: !(params.known_indels)
 
     script:
     """

From 944ea5560a412fc64ffdf247e62b3bace918cfcb Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 19 Mar 2020 10:56:53 +0100
Subject: [PATCH 02/23] check for all references

---
 main.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 5ce59d2ace..8178ee9f86 100644
--- a/main.nf
+++ b/main.nf
@@ -331,8 +331,10 @@ if (params.vepCacheVersion) exit 1, "The params `--vepCacheVersion` has been rem
 */
 
 // Check if genome exists in the config file
-if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+if (params.genomes && params.genome && !params.genomes.containsKey(params.genome) && !params.igenomes_ignore) {
     exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
+else if (params.genomes && params.genome && !params.genomes.containsKey(params.genome) && params.igenomes_ignore) {
+    exit 1, "The provided genome '${params.genome}' is not available in the genomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
 }
 
 stepList = defineStepList()
@@ -564,6 +566,7 @@ if (params.monochrome_logs) log.info "------------------------------------------
 else log.info "-\033[2m--------------------------------------------------\033[0m-"
 
 if ('mutect2' in tools && !(params.pon)) log.warn "[nf-core/sarek] Mutect2 was requested, but as no panel of normals were given, results will not be optimal"
+if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works if Sentieon is available where nf-core/sarek is run"
 
 // Check the hostnames against configured profiles
 checkHostname()

From 8ebf631afd5bb698ba368216a44172415ee622bc Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Mar 2020 15:12:17 +0100
Subject: [PATCH 03/23] update docs

---
 docs/usage.md | 2 +-
 main.nf       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 653787c914..7dea171d8c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -323,7 +323,7 @@ Available: `mapping`, `recalibrate`, `variantcalling` and `annotate`
 ### --tools
 
 Use this to specify the tools to run:
-Available: `ASCAT`, `ControlFREEC`, `FreeBayes`, `HaplotypeCaller`, `Manta`, `mpileup`, `Mutect2`, `Strelka`, `TIDDIT`
+Available: `ASCAT`, `ControlFREEC`, `FreeBayes`, `HaplotypeCaller`, `Manta`, `mpileup`, `MSIsensor`, `Mutect2`, `Strelka`, `TIDDIT`
 
 ### --sentieon
 
diff --git a/main.nf b/main.nf
index 3a2b9363a0..9324168286 100644
--- a/main.nf
+++ b/main.nf
@@ -53,7 +53,7 @@ def helpMessage() {
       --target_bed             [file] Target BED file for targeted or whole exome sequencing
       --tools                   [str] Specify tools to use for variant calling:
                                       Available: ASCAT, ControlFREEC, FreeBayes, HaplotypeCaller
-                                      Manta, mpileup, Mutect2, Strelka, TIDDIT
+                                      Manta, mpileup, MSIsensor, Mutect2, Strelka, TIDDIT
                                       and/or for annotation:
                                       snpEff, VEP, merge
                                       Default: None

From ebd4840a69267c80a1f5572e9bc3d88c83edcb8d Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Mar 2020 16:37:30 +0100
Subject: [PATCH 04/23] indentation

---
 main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 9324168286..f39e5043a8 100644
--- a/main.nf
+++ b/main.nf
@@ -2234,11 +2234,11 @@ process ConcatVCF {
 
     script:
     if (variantCaller == 'HaplotypeCallerGVCF')
-          outputFile = "HaplotypeCaller_${idSample}.g.vcf"
+        outputFile = "HaplotypeCaller_${idSample}.g.vcf"
     else if (variantCaller == "Mutect2")
-          outputFile = "Mutect2_unfiltered_${idSample}.vcf"
+        outputFile = "Mutect2_unfiltered_${idSample}.vcf"
     else
-          outputFile = "${variantCaller}_${idSample}.vcf"
+        outputFile = "${variantCaller}_${idSample}.vcf"
     options = params.target_bed ? "-t ${targetBED}" : ""
     intervalsOptions = params.no_intervals ? "-n" : ""
     """

From 6ed31e4332677508b5bfd9bf6cd13d8853919ec5 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Mar 2020 16:38:25 +0100
Subject: [PATCH 05/23] sort contributors

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5b561495d5..2463d6d5e1 100644
--- a/README.md
+++ b/README.md
@@ -85,6 +85,7 @@ Helpful contributors:
 * [Adrian Lärkeryd](https://github.com/adrlar)
 * [Alexander Peltzer](https://github.com/apeltzer)
 * [Chela James](https://github.com/chelauk)
+* [David Mas-Ponte](https://github.com/davidmasp)
 * [Francesco L](https://github.com/nibscles)
 * [FriederikeHanssen](https://github.com/FriederikeHanssen)
 * [Gisela Gabernet](https://github.com/ggabernet)
@@ -105,7 +106,6 @@ Helpful contributors:
 * [gulfshores](https://github.com/gulfshores)
 * [pallolason](https://github.com/pallolason)
 * [silviamorins](https://github.com/silviamorins)
-* [David Mas-Ponte](https://github.com/davidmasp)
 
 ## Contributions & Support
 

From c366622211d014a88a100fc755d72306343a0ef3 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Mar 2020 17:18:05 +0100
Subject: [PATCH 06/23] more comments

---
 main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index f39e5043a8..c43941a418 100644
--- a/main.nf
+++ b/main.nf
@@ -333,7 +333,7 @@ if (params.vepCacheVersion) exit 1, "The params `--vepCacheVersion` has been rem
 // Check if genome exists in the config file
 if (params.genomes && params.genome && !params.genomes.containsKey(params.genome) && !params.igenomes_ignore) {
     exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
-else if (params.genomes && params.genome && !params.genomes.containsKey(params.genome) && params.igenomes_ignore) {
+} else if (params.genomes && params.genome && !params.genomes.containsKey(params.genome) && params.igenomes_ignore) {
     exit 1, "The provided genome '${params.genome}' is not available in the genomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
 }
 
@@ -409,8 +409,9 @@ if (tsvPath) {
     }
 } else if (params.input && !hasExtension(params.input, "tsv")) {
     log.info "No TSV file"
-    if (step != 'mapping') exit 1, 'No other step than "mapping" support a dir as an input'
+    if (step != 'mapping') exit 1, 'No other step than "mapping" support a directory as an input'
     log.info "Reading ${params.input} directory"
+    log.warn "[nf-core/sarek] in ${params.input} directory, all fastqs are assuming to be from the same sample, which is assumed to be a germline one"
     inputSample = extractFastqFromDir(params.input)
     (inputSample, fastqTMP) = inputSample.into(2)
     fastqTMP.toList().subscribe onNext: {

From c3e40d1c930394f291dcd7daafef0dc225fe150c Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Mar 2020 17:30:16 +0100
Subject: [PATCH 07/23] fix links to GTA CI

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2463d6d5e1..e5f8edd1dc 100644
--- a/README.md
+++ b/README.md
@@ -4,8 +4,8 @@
 [![nf-core](https://img.shields.io/badge/nf--core-pipeline-brightgreen.svg)](https://nf-co.re/)
 [![DOI](https://zenodo.org/badge/184289291.svg)](https://zenodo.org/badge/latestdoi/184289291)
 
-[![GitHub Actions CI status](https://github.com/nf-core/sarek/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22sarek+CI%22)
-[![GitHub Actions Linting status](https://github.com/nf-core/sarek/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22sarek+linting%22)
+[![GitHub Actions CI status](https://github.com/nf-core/sarek/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting status](https://github.com/nf-core/sarek/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22)
 [![CircleCi build status](https://img.shields.io/circleci/project/github/nf-core/sarek?logo=circleci)](https://circleci.com/gh/nf-core/sarek/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)

From cba78ab777de0f5c3ad08aabb571e1502a845860 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 23 Mar 2020 09:44:43 +0100
Subject: [PATCH 08/23] add vcf concatenated to annotation

---
 main.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/main.nf b/main.nf
index c43941a418..43fe1344e5 100644
--- a/main.nf
+++ b/main.nf
@@ -2968,6 +2968,10 @@ controlFreecVizOut.dump(tag:'ControlFreecViz')
 (vcfMantaSomaticSV, vcfMantaDiploidSV) = vcfManta.into(2)
 
 vcfKeep = Channel.empty().mix(
+    vcfConcatenated.map{
+        variantcaller, idPatient, idSample, vcf, tbi ->
+        [variantcaller, idSample, vcf]
+    },
     vcfSentieon.map {
         variantcaller, idPatient, idSample, vcf, tbi ->
         [variantcaller, idSample, vcf]

From b9c37ee3c8bb7100fa825135922ee9d400077ea6 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 25 Mar 2020 16:32:30 +0100
Subject: [PATCH 09/23] typo

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 1ea5dd160a..1a6d96840f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -36,7 +36,7 @@ params {
   single_end = false // No single end
 
   // Preprocessing
-  markdup_java_options = '"-Xms4000m -Xmx7g"' // Established values for markDuplicate memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details
+  markdup_java_options = '"-Xms4000m -Xmx7g"' // Established values for markDuplicates memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details
   sentieon = null // Not using Sentieon by default
   sequencing_center = null // No sequencing center to be written in BAM header in MapReads process
 

From d0b820f170b4ea93df645a841988e3eb0c8c2684 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 26 Mar 2020 16:21:38 +0100
Subject: [PATCH 10/23] typo

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 43fe1344e5..62004ec8a4 100644
--- a/main.nf
+++ b/main.nf
@@ -126,7 +126,7 @@ def helpMessage() {
 
     AWSBatch options:
       --awsqueue                [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch
-      --awsregion               [str] The AWS Region for your AWS Batch job to run on
+      --awsregion               [str] The AWS Region for your AWSBatch job to run on
       --awscli                  [str] Path to the AWS CLI tool
     """.stripIndent()
 }

From b33446e7d863fc98d01ff0e9599b3f9adca289e4 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 26 Mar 2020 16:22:06 +0100
Subject: [PATCH 11/23] update gatkspark from 4.1.4.1 to 4.1.6.0

---
 docs/containers.md | 2 +-
 environment.yml    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/containers.md b/docs/containers.md
index 0d2aa08539..ce8ec759de 100644
--- a/docs/containers.md
+++ b/docs/containers.md
@@ -21,7 +21,7 @@ For annotation, the main container can be used, but the cache has to be download
 - Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.5
 - Contain **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** 0.11.9
 - Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.3.2
-- Contain **[GATK4-spark](https://github.com/broadinstitute/gatk)** 4.1.4.1
+- Contain **[GATK4-spark](https://github.com/broadinstitute/gatk)** 4.1.6.0
 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
 - Contain **[ggplot2](https://github.com/tidyverse/ggplot2)** 3.3.0
 - Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9
diff --git a/environment.yml b/environment.yml
index c1889a8476..ef0f9c6b59 100644
--- a/environment.yml
+++ b/environment.yml
@@ -17,7 +17,7 @@ dependencies:
   - bioconda::ensembl-vep=99.2
   - bioconda::fastqc=0.11.9
   - bioconda::freebayes=1.3.2
-  - bioconda::gatk4-spark=4.1.4.1
+  - bioconda::gatk4-spark=4.1.6.0
   - bioconda::genesplicer=1.0
   - bioconda::htslib=1.9
   - bioconda::manta=1.6.0

From 3a4f3c7ac7a9cea121efd3c27fc6fe1796e627fe Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 26 Mar 2020 17:33:19 +0100
Subject: [PATCH 12/23] test changing URLs

---
 conf/test.config            | 4 ++--
 conf/test_annotation.config | 2 +-
 conf/test_targeted.config   | 2 +-
 conf/test_tool.config       | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index a21421087c..6f3fd815c8 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -17,12 +17,12 @@ params {
   max_time = 48.h
 
   // Input data
-  input = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/tsv/tiny-manta-https.tsv'
+  input = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv'
 
   // Small reference genome
   igenomes_ignore = true
   genome = 'smallGRCh37'
-  genomes_base = "https://github.com/nf-core/test-datasets/raw/sarek/reference"
+  genomes_base = "https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/reference"
 }
 
 process {
diff --git a/conf/test_annotation.config b/conf/test_annotation.config
index e9955c420b..1028e7909b 100644
--- a/conf/test_annotation.config
+++ b/conf/test_annotation.config
@@ -11,5 +11,5 @@ includeConfig 'test.config'
 
 params {
   genome            = 'WBcel235'
-  input             = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
+  input             = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
 }
\ No newline at end of file
diff --git a/conf/test_targeted.config b/conf/test_targeted.config
index 2daa595512..b6f2c59180 100644
--- a/conf/test_targeted.config
+++ b/conf/test_targeted.config
@@ -10,6 +10,6 @@
 includeConfig 'test.config'
 
 params {
-  target_bed = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/target.bed'
+  target_bed = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/target.bed'
   tools = 'manta,strelka'
 }
\ No newline at end of file
diff --git a/conf/test_tool.config b/conf/test_tool.config
index fa51779592..6e1ff9f47c 100644
--- a/conf/test_tool.config
+++ b/conf/test_tool.config
@@ -11,6 +11,6 @@ includeConfig 'test.config'
 
 params {
   // Input data
-  input = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/tsv/tiny-recal-pair-https.tsv'
+  input = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/tsv/tiny-recal-pair-https.tsv'
   step = 'variantcalling'
 }
\ No newline at end of file

From 3ba97c7dbe7aa41660904ae26c8faba191e63fc4 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 26 Mar 2020 17:47:10 +0100
Subject: [PATCH 13/23] update URLs

---
 conf/genomes.config         | 2 +-
 conf/test.config            | 4 ++--
 conf/test_annotation.config | 2 +-
 conf/test_targeted.config   | 2 +-
 conf/test_tool.config       | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/conf/genomes.config b/conf/genomes.config
index 683a496882..d9d5afee37 100644
--- a/conf/genomes.config
+++ b/conf/genomes.config
@@ -55,7 +55,7 @@ params {
     'smallGRCh37' {
       dbsnp                   = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
       fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
-      germline_resource       = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
+      germline_resource       = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.small.PASS.AC.AF.only.vcf.gz"
       intervals               = "${params.genomes_base}/small.intervals"
       known_indels            = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
       snpeff_db               = 'GRCh37.87'
diff --git a/conf/test.config b/conf/test.config
index 6f3fd815c8..3e656a5fdc 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -17,12 +17,12 @@ params {
   max_time = 48.h
 
   // Input data
-  input = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv'
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv'
 
   // Small reference genome
   igenomes_ignore = true
   genome = 'smallGRCh37'
-  genomes_base = "https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/reference"
+  genomes_base = "https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference"
 }
 
 process {
diff --git a/conf/test_annotation.config b/conf/test_annotation.config
index 1028e7909b..70400f3182 100644
--- a/conf/test_annotation.config
+++ b/conf/test_annotation.config
@@ -11,5 +11,5 @@ includeConfig 'test.config'
 
 params {
   genome            = 'WBcel235'
-  input             = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
+  input             = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
 }
\ No newline at end of file
diff --git a/conf/test_targeted.config b/conf/test_targeted.config
index b6f2c59180..9045068145 100644
--- a/conf/test_targeted.config
+++ b/conf/test_targeted.config
@@ -10,6 +10,6 @@
 includeConfig 'test.config'
 
 params {
-  target_bed = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/target.bed'
+  target_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/target.bed'
   tools = 'manta,strelka'
 }
\ No newline at end of file
diff --git a/conf/test_tool.config b/conf/test_tool.config
index 6e1ff9f47c..dfe5d7d4c0 100644
--- a/conf/test_tool.config
+++ b/conf/test_tool.config
@@ -11,6 +11,6 @@ includeConfig 'test.config'
 
 params {
   // Input data
-  input = 'https://raw.githubusercontent.com/MaxUlysse/nf-core_test-datasets/sarek/testdata/tsv/tiny-recal-pair-https.tsv'
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-recal-pair-https.tsv'
   step = 'variantcalling'
 }
\ No newline at end of file

From 748e156b6fd27b8a678d3e00c984809b63e2a346 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 09:33:16 +0100
Subject: [PATCH 14/23] add --no_gatk_spark params

---
 docs/usage.md | 16 +++++++++++-----
 main.nf       | 17 ++++++++++++++++-
 2 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 7dea171d8c..6087b803f1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -20,6 +20,7 @@
   - [--annotateVCF](#--annotatevcf)
   - [--no_gvcf](#--no_gvcf)
   - [--noGVCF](#--nogvcf)
+  - [--no_gatk_spark](#--no_gatk_spark)
   - [--skip_qc](#--skip_qc)
   - [--skipQC](#--skipqc)
   - [--noReports](#--noreports)
@@ -78,7 +79,7 @@
 - [Job resources](#job-resources)
   - [Automatic resubmission](#automatic-resubmission)
   - [Custom resource requests](#custom-resource-requests)
-- [AWS Batch specific parameters](#aws-batch-specific-parameters)
+- [AWSBatch specific parameters](#awsbatch-specific-parameters)
   - [--awsqueue](#--awsqueue)
   - [--awsregion](#--awsregion)
   - [--awscli](#--awscli)
@@ -289,6 +290,10 @@ Use this to disable g.vcf from `HaplotypeCaller`.
 > :warning: This params is deprecated -- it will be removed in a future release.
 > Please check: [`--no_gvcf`](#--no_gvcf)
 
+### --no_gatk_spark
+
+Use this to disable usage of GATK Spark implementation of their tools in local mode.
+
 ### --skip_qc
 
 Use this to disable specific QC and Reporting tools.
@@ -772,14 +777,14 @@ You can then create a pull request to the `nf-core/configs` repository with the
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).
 
-## AWS Batch specific parameters
+## AWSBatch specific parameters
 
-Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration.
+Running the pipeline on AWSBatch requires a couple of specific parameters to be set according to your AWSBatch configuration.
 Please use [`-profile awsbatch`](https://github.com/nf-core/configs/blob/master/conf/awsbatch.config) and then specify all of the following parameters.
 
 ### --awsqueue
 
-The JobQueue that you intend to use on AWS Batch.
+The JobQueue that you intend to use on AWSBatch.
 
 ### --awsregion
 
@@ -788,7 +793,8 @@ Default is set to `eu-west-1` but can be adjusted to your needs.
 
 ### --awscli
 
-The [AWS CLI](https://www.nextflow.io/docs/latest/awscloud.html#aws-cli-installation) path in your custom AMI. Default: `/home/ec2-user/miniconda/bin/aws`.
+The [AWS CLI](https://www.nextflow.io/docs/latest/awscloud.html#aws-cli-installation) path in your custom AMI.
+Default: `/home/ec2-user/miniconda/bin/aws`.
 
 Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
 
diff --git a/main.nf b/main.nf
index 62004ec8a4..28e57815dc 100644
--- a/main.nf
+++ b/main.nf
@@ -48,6 +48,7 @@ def helpMessage() {
       --no_gvcf                [bool] No g.vcf output from HaplotypeCaller
       --no_strelka_bp          [bool] Will not use Manta candidateSmallIndels for Strelka as Best Practice
       --no_intervals           [bool] Disable usage of intervals
+      --no_gatk_spark          [bool] Disable usage of GATK Spark implementation of their tools in local mode
       --nucleotides_per_second  [int] To estimate interval size
                                       Default: 1000.0
       --target_bed             [file] Target BED file for targeted or whole exome sequencing
@@ -1236,7 +1237,7 @@ process IndexBamFile {
 
 // STEP 2: MARKING DUPLICATES
 
-process MarkDuplicatesSpark {
+process MarkDuplicates {
     label 'cpus_16'
 
     tag {idPatient + "-" + idSample}
@@ -1259,6 +1260,19 @@ process MarkDuplicatesSpark {
     script:
     markdup_java_options = task.memory.toGiga() > 8 ? params.markdup_java_options : "\"-Xms" +  (task.memory.toGiga() / 2).trunc() + "g -Xmx" + (task.memory.toGiga() - 1) + "g\""
     metrics = 'markduplicates' in skipQC ? '' : "-M ${idSample}.bam.metrics"
+    if (params.no_gatk_spark)
+    """
+    gatk --java-options ${markdup_java_options} \
+        MarkDuplicates \
+        --MAX_RECORDS_IN_RAM 50000 \
+        --INPUT ${idSample}.bam \
+        --METRICS_FILE ${idSample}.bam.metrics \
+        --TMP_DIR . \
+        --ASSUME_SORT_ORDER coordinate \
+        --CREATE_INDEX true \
+        --OUTPUT ${idSample}.md.bam
+    """
+    else
     """
     gatk --java-options ${markdup_java_options} \
         MarkDuplicatesSpark \
@@ -1267,6 +1281,7 @@ process MarkDuplicatesSpark {
         ${metrics} \
         --tmp-dir . \
         --create-output-bam-index true
+        --spark-master local[${task.cpus}]
     """
 }
 

From b9d41c25597fc66da700fb4df1bfc533aa0578d1 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 09:47:04 +0100
Subject: [PATCH 15/23] add tests for GATKspark

---
 .github/workflows/ci.yml                           |  2 +-
 conf/test_annotation.config                        |  2 +-
 conf/test_no_gatk_spark.config                     | 14 ++++++++++++++
 ...t_splitfastq.config => test_split_fastq.config} |  2 +-
 conf/test_targeted.config                          |  2 +-
 conf/test_tool.config                              |  2 +-
 conf/test_trimming.config                          |  2 +-
 nextflow.config                                    |  1 +
 8 files changed, 21 insertions(+), 6 deletions(-)
 create mode 100644 conf/test_no_gatk_spark.config
 rename conf/{test_splitfastq.config => test_split_fastq.config} (84%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 71d634521f..6c658ca202 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -108,7 +108,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        profile: [test_splitfastq, test_targeted, test_trimming]
+        profile: [test_split_fastq, test_targeted, test_trimming, test_no_gatk_spark]
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
diff --git a/conf/test_annotation.config b/conf/test_annotation.config
index 70400f3182..4508b0eeef 100644
--- a/conf/test_annotation.config
+++ b/conf/test_annotation.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test
+ *   nextflow run nf-core/sarek -profile test_annotation
  */
 
 includeConfig 'test.config'
diff --git a/conf/test_no_gatk_spark.config b/conf/test_no_gatk_spark.config
new file mode 100644
index 0000000000..877d44f0d6
--- /dev/null
+++ b/conf/test_no_gatk_spark.config
@@ -0,0 +1,14 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/sarek -profile test_no_gatk_spark
+ */
+
+includeConfig 'test.config'
+
+params {
+  no_gatk_spark = true
+}
\ No newline at end of file
diff --git a/conf/test_splitfastq.config b/conf/test_split_fastq.config
similarity index 84%
rename from conf/test_splitfastq.config
rename to conf/test_split_fastq.config
index 5209ec401b..73d1dfc1d4 100644
--- a/conf/test_splitfastq.config
+++ b/conf/test_split_fastq.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test
+ *   nextflow run nf-core/sarek -profile test_no_split_fastq
  */
 
 includeConfig 'test.config'
diff --git a/conf/test_targeted.config b/conf/test_targeted.config
index 9045068145..e39e9f91eb 100644
--- a/conf/test_targeted.config
+++ b/conf/test_targeted.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_targeted
+ *   nextflow run nf-core/sarek -profile test_no_split_fastq
  */
 
 includeConfig 'test.config'
diff --git a/conf/test_tool.config b/conf/test_tool.config
index dfe5d7d4c0..3d9a934533 100644
--- a/conf/test_tool.config
+++ b/conf/test_tool.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test
+ *   nextflow run nf-core/sarek -profile test_tool
  */
 
 includeConfig 'test.config'
diff --git a/conf/test_trimming.config b/conf/test_trimming.config
index 8192ee4b79..f9a4af2da2 100644
--- a/conf/test_trimming.config
+++ b/conf/test_trimming.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test
+ *   nextflow run nf-core/sarek -profile test_trimming
  */
 
 includeConfig 'test.config'
diff --git a/nextflow.config b/nextflow.config
index 1a6d96840f..80d564b4b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -36,6 +36,7 @@ params {
   single_end = false // No single end
 
   // Preprocessing
+  no_gatk_spark = null // GATK Spark implementation of their tools in local mode used by default
   markdup_java_options = '"-Xms4000m -Xmx7g"' // Established values for markDuplicates memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details
   sentieon = null // Not using Sentieon by default
   sequencing_center = null // No sequencing center to be written in BAM header in MapReads process

From aa2b772ef4de0ce2a5ddaba010fc0ccdb4108109 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 09:48:45 +0100
Subject: [PATCH 16/23] fix typo

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 28e57815dc..bd4f2fac78 100644
--- a/main.nf
+++ b/main.nf
@@ -1280,7 +1280,7 @@ process MarkDuplicates {
         -O ${idSample}.md.bam \
         ${metrics} \
         --tmp-dir . \
-        --create-output-bam-index true
+        --create-output-bam-index true \
         --spark-master local[${task.cpus}]
     """
 }

From 4a205692956ff54c8e4ade6bc6609bc49ed0a166 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 09:52:34 +0100
Subject: [PATCH 17/23] fix paths to files

---
 nextflow.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 80d564b4b2..2b88d57f0f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -145,7 +145,8 @@ profiles {
   }
   test { includeConfig 'conf/test.config' }
   test_annotation { includeConfig 'conf/test_annotation.config' }
-  test_splitfastq { includeConfig 'conf/test_splitfastq.config' }
+  test_no_gatk_spark { includeConfig 'conf/test_no_gatk_spark.config' }
+  test_split_fastq { includeConfig 'conf/test_split_fastq.config' }
   test_targeted { includeConfig 'conf/test_targeted.config' }
   test_tool { includeConfig 'conf/test_tool.config' }
   test_trimming { includeConfig 'conf/test_trimming.config' }

From c04093c967f0a48fcbadfe46954acea553fda37f Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 10:06:09 +0100
Subject: [PATCH 18/23] typo in params name

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index bd4f2fac78..a5cb5fa966 100644
--- a/main.nf
+++ b/main.nf
@@ -506,7 +506,7 @@ if (params.trim_fastq) {
     summary["Trim 3' R1"]         = "${params.three_prime_clip_r1} bp"
     summary["Trim 3' R2"]         = "${params.three_prime_clip_r2} bp"
     summary["NextSeq Trim"]       = "${params.trim_nextseq} bp"
-    summary['Saved Trimmed Fastq'] = params.saveTrimmed ? 'Yes' : 'No'
+    summary['Saved Trimmed Fastq'] = params.save_trimmed ? 'Yes' : 'No'
 }
 
 if (params.no_intervals && step != 'annotate') summary['Intervals']         = 'Do not use'

From 0fe3e23d35acca31287fad4f24ba43d1356a7e04 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 10:16:46 +0100
Subject: [PATCH 19/23] fix MarkDuplicates output with --no_gatk_spark params

---
 .github/workflows/ci.yml | 8 ++++----
 main.nf                  | 6 ++++--
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6c658ca202..9a96bf84a7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,7 +50,7 @@ jobs:
           docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
           docker tag nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }} nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
       - name: Run annotation test
-        run: nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.tools }}
+        run: nextflow run . -profile test_annotation,docker --tools ${{ matrix.tools }}
 
   germline:
     env:
@@ -100,7 +100,7 @@ jobs:
           docker pull nfcore/sarek:dev
           docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test for minimal genomes
-        run: nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
+        run: nextflow run . -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
   profile:
     env:
@@ -123,7 +123,7 @@ jobs:
           docker pull nfcore/sarek:dev
           docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.profile }} test
-        run: nextflow run . -profile ${{ matrix.profile }},docker --verbose
+        run: nextflow run . -profile ${{ matrix.profile }},docker
 
   tools:
     env:
@@ -146,4 +146,4 @@ jobs:
           docker pull nfcore/sarek:dev
           docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.tool }} test
-        run: nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}
+        run: nextflow run . -profile test_tool,docker --tools ${{ matrix.tool }}
diff --git a/main.nf b/main.nf
index a5cb5fa966..f72782ec34 100644
--- a/main.nf
+++ b/main.nf
@@ -1271,6 +1271,8 @@ process MarkDuplicates {
         --ASSUME_SORT_ORDER coordinate \
         --CREATE_INDEX true \
         --OUTPUT ${idSample}.md.bam
+    
+    mv ${idSample}.md.bai ${idSample}.md.bam.bai
     """
     else
     """
@@ -2637,7 +2639,7 @@ vcfStrelkaBP = vcfStrelkaBP.dump(tag:'Strelka BP')
 // STEP MSISENSOR.1 - SCAN
 
 // Scan reference genome for microsattelites
-process msisensorScan {
+process MSIsensor_scan {
     label 'cpus_1'
     label 'memory_max'
     // memory '20 GB'
@@ -2663,7 +2665,7 @@ process msisensorScan {
 
 // Score the normal vs somatic pair of bams
 
-process msisensor {
+process MSIsensor_msi {
     label 'cpus_4'
     label 'memory_max'
     // memory '10 GB'

From de36812c17f3880dd963396aa33fe8b7e68dcc04 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 10:24:51 +0100
Subject: [PATCH 20/23] fix comments

---
 .github/workflows/ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9a96bf84a7..40ea2ff40c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,7 +41,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          # Only check Nextflow pipeline minimum version for other C
+          # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
@@ -63,7 +63,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          # Only check Nextflow pipeline minimum version for other C
+          # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
@@ -93,7 +93,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          # Only check Nextflow pipeline minimum version for other C
+          # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
@@ -116,7 +116,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          # Only check Nextflow pipeline minimum version for other C
+          # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
@@ -131,7 +131,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tool: [Haplotypecaller, Freebayes, Manta, mpileup, Strelka, TIDDIT, msisensor]
+        tool: [Haplotypecaller, Freebayes, Manta, mpileup, Strelka, TIDDIT, MSIsensor]
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
@@ -139,7 +139,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
-          # Only check Nextflow pipeline minimum version for other C
+          # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |

From 0cc3726c0c0e809b7eaf9a244029ffb1ab693812 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 10:53:31 +0100
Subject: [PATCH 21/23] improve CHANGELOG

---
 CHANGELOG.md | 119 +++++++++++++++++++++++++++------------------------
 1 file changed, 62 insertions(+), 57 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 50cb7de2fd..e3139fc58d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 
 ## dev
 
-### `Added`
+### Added
 
 - [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
 - [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
@@ -14,10 +14,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
 - [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235`
 - [#150](https://github.com/nf-core/sarek/pull/150), [#151](https://github.com/nf-core/sarek/pull/151), [#154](https://github.com/nf-core/sarek/pull/154) - Add AWS mega test GitHub Actions
-- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` v `3.3.0`
-- [#163](https://github.com/nf-core/sarek/pull/163) - Add [msisensor](https://github.com/ding-lab/msisensor) in tools and container
+- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` version `3.3.0`
+- [#163](https://github.com/nf-core/sarek/pull/163) - Add [MSIsensor](https://github.com/ding-lab/msisensor) in tools and container
+- [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests
 
-### `Changed`
+### Changed
 
 - [#76](https://github.com/nf-core/sarek/pull/76) - Use `MarkDuplicatesSpark` instead of `MarkDuplicates`
 - [#76](https://github.com/nf-core/sarek/pull/76) - Use `gatk4-spark` instead of `gatk4` in `environment.yml`
@@ -37,14 +38,16 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `Manta` to `1.6.0`
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `Qualimap` to `2.2.2d`
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `VEP` to `99.2`
-- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `87` for `GRCh37`
-- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `92` for `GRCh38`
+- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version from `75` to `87` for `GRCh37`
+- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version from `86` to `92` for `GRCh38`
 - [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
 - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
 - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
 - [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158) - Update docs
+- [#164](https://github.com/nf-core/sarek/pull/164) - Update `gatk4-spark` from `4.1.4.1` to `4.1.6.0`
+- [#164](https://github.com/nf-core/sarek/pull/164) - Update docs
 
-### `Fixed`
+### Fixed
 
 - [#83](https://github.com/nf-core/sarek/pull/83) - Fix some typos in `docs/input.md`
 - [#107](https://github.com/nf-core/sarek/pull/107) - Fix linting
@@ -63,8 +66,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#156](https://github.com/nf-core/sarek/pull/156) - Fix typos
 - [#156](https://github.com/nf-core/sarek/pull/156) - Fix issues with `dbsnp` files while using only `Sention` tools
 - [#158](https://github.com/nf-core/sarek/pull/158) - Fix typo with `params.snpeff_cache` to decide containers for `snpEff`
+- [#164](https://github.com/nf-core/sarek/pull/164) - Fix issues when running with `Sentieon`
+- [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
 
-### `Deprecated`
+### Deprecated
 
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--annotateTools` is now deprecated, use `--annotate_tools` instead
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_InDels` is now deprecated, use `--cadd_indels` instead
@@ -81,7 +86,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--snpEff_cache` is now deprecated, use `--snpeff_cache` instead
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--targetBed` is now deprecated, use `--target_bed` instead
 
-### `Removed`
+### Removed
 
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--acLociGC` is now removed, use `--ac_loci_gc` instead
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--acLoci` is now removed, use `--ac_loci` instead
@@ -107,7 +112,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 
 Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 
-### `Added`
+### Added - [2.5.2]
 
 - [#45](https://github.com/nf-core/sarek/pull/45) - Include Workflow figure in `README.md`
 - [#46](https://github.com/nf-core/sarek/pull/46) - Add location to abstracts
@@ -122,7 +127,7 @@ Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 - [#61](https://github.com/nf-core/sarek/pull/61) - Add test `SPLITFASTQ`
 - [#66](https://github.com/nf-core/sarek/pull/66) - Add `Sentieon` possibilities to Sarek
 
-### `Changed`
+### Changed - [2.5.2]
 
 - [#54](https://github.com/nf-core/sarek/pull/54) - Bump version to `2.5.2dev`
 - [#60](https://github.com/nf-core/sarek/pull/60) - Some process (`BaseRecalibrator`, `ApplyBQSR`, `Mpileup`) have now optional usage of interval files
@@ -133,13 +138,13 @@ Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 - [#74](https://github.com/nf-core/sarek/pull/74) - Improve CI tests (both Jenkins and GitHub actions tests)
 - [#74](https://github.com/nf-core/sarek/pull/74) - Move all CI from `ci-extra.yml` to `ci.yml`
 
-### `Removed`
+### Removed - [2.5.2]
 
 - [#46](https://github.com/nf-core/sarek/pull/46) - Remove mention of old `build.nf` script which was included in `main.nf`
 - [#74](https://github.com/nf-core/sarek/pull/74) - Remove `download_image.sh` and `run_tests.sh` scripts
 - [#76](https://github.com/nf-core/sarek/pull/76) - Remove `runOptions = "-u \$(id -u):\$(id -g)"` in `nextflow.config` to enable `Spark` possibilities
 
-### `Fixed`
+### Fixed - [2.5.2]
 
 - [#40](https://github.com/nf-core/sarek/pull/40) - Fix issue with `publishDirMode` within `test` profile
 - [#42](https://github.com/nf-core/sarek/pull/42) - Fix typos, and minor updates in `README.md`
@@ -153,11 +158,11 @@ Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 
 Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.
 
-### `Added`
+### Added - [2.5.1]
 
 - [#53](https://github.com/nf-core/sarek/pull/53) - Release `2.5.1`
 
-### `Fixed`
+### Fixed - [2.5.1]
 
 - [#48](https://github.com/nf-core/sarek/issues/48) - Fix `singularity.autoMounts` issue.
 - [#49](https://github.com/nf-core/sarek/issues/49) - Use correct tag for annotation containers.
@@ -169,7 +174,7 @@ Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.
 
-### `Added`
+### Added - [2.5]
 
 - [#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), [#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`
@@ -208,7 +213,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#31](https://github.com/nf-core/sarek/pull/31) - Add extra CI to `GitHub Actions` nf-core extra CI
 - [#35](https://github.com/nf-core/sarek/pull/35) - Building indexes from [nf-core/test-datasets:sarek](https://github.com/nf-core/test-datasets/tree/sarek) for CI and small tests
 
-### `Changed`
+### Changed - [2.5]
 
 - [#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), [#21](https://github.com/nf-core/sarek/pull/21), [#23](https://github.com/nf-core/sarek/pull/23), [#29](https://github.com/nf-core/sarek/pull/29) - Update docs
 - [#4](https://github.com/nf-core/sarek/pull/4) - Update `cancerit-allelecount` from `2.1.2` to `4.0.2`
@@ -253,7 +258,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#37](https://github.com/nf-core/sarek/pull/37) - Bump version for Release
 - [#38](https://github.com/nf-core/sarek/pull/38) - File names before merge is based on `${idSample}_${idRun}` instead of `${idRun}`
 
-### `Removed`
+### Removed - [2.5]
 
 - [#9](https://github.com/nf-core/sarek/pull/9) - Removed `relatedness2` graph from `vcftools stats`
 - [#13](https://github.com/nf-core/sarek/pull/13) - Removed `BamQCmapped` and `BamQCrecalibrated` processes
@@ -268,7 +273,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#35](https://github.com/nf-core/sarek/pull/35) - Remove `Mutect2` from `MULTIPLE` test
 - [#35](https://github.com/nf-core/sarek/pull/35) - Remove `referenceMap` and `defineReferenceMap()` and use Channel values instead
 
-### `Fixed`
+### Fixed - [2.5]
 
 - [#3](https://github.com/nf-core/sarek/pull/3) - Fix `Docker` ownership
 - [#11](https://github.com/nf-core/sarek/pull/11) - Fix `MergeMpileup` PublishDir
@@ -287,7 +292,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#38](https://github.com/nf-core/sarek/pull/38) - Avoid collision in `MultiQC`
 - [#39](https://github.com/nf-core/sarek/pull/39) - Fix `ch_dbsnp` channel
 
-### `Deprecated`
+### Deprecated - [2.5]
 
 - [#23](https://github.com/nf-core/sarek/pull/23) - `--sample` is now deprecated, use `--input` instead
 - [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeFile` is now deprecated, use `--fasta` instead
@@ -297,7 +302,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 
 ## [2.3.FIX1] - 2019-03-04
 
-### `Fixed`
+### Fixed - [2.3.FIX1]
 
 - [#742](https://github.com/SciLifeLab/Sarek/pull/742) - Fix output dirs (`HaplotypeCaller` that was not recognized by `annotate.nf` introduced by [#728](https://github.com/SciLifeLab/Sarek/pull/728))
 
@@ -305,7 +310,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 
 Äpar is one of the main massif in the Sarek National Park.
 
-### `Added`
+### Added - [2.3]
 
 - [#628](https://github.com/SciLifeLab/Sarek/pull/628), [#722](https://github.com/SciLifeLab/Sarek/pull/722) - `ASCAT` now use `.gc` file
 - [#712](https://github.com/SciLifeLab/Sarek/pull/712), [#718](https://github.com/SciLifeLab/Sarek/pull/718) - Added possibilities to run Sarek with `conda`
@@ -324,7 +329,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#735](https://github.com/SciLifeLab/Sarek/pull/735) - Added `--exome` for `Manta`, and for `StrelkaBP`
 - [#735](https://github.com/SciLifeLab/Sarek/pull/735) - Added `Travis CI` test for targeted
 
-### `Changed`
+### Changed - [2.3]
 
 - [#710](https://github.com/SciLifeLab/Sarek/pull/710) - Improve release checklist and script
 - [#711](https://github.com/SciLifeLab/Sarek/pull/711) - Improve configuration priorities
@@ -347,7 +352,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Reduce number of CPUs for `RunVEP` to `4` cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)
 - [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Update `VEP` from `95.1` to `95.2`
 
-### `Removed`
+### Removed - [2.3]
 
 - [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf`
 - [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpEff` base container is no longer used
@@ -355,7 +360,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Remove `defineDirectoryMap()`
 - [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Remove `--database` option for VEP cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)
 
-### `Fixed`
+### Fixed - [2.3]
 
 - [#720](https://github.com/SciLifeLab/Sarek/pull/720) - `bamQC` is now run on the recalibrated bams, and not after `MarkDuplicates`
 - [#726](https://github.com/SciLifeLab/Sarek/pull/726) - Fix `Ascat` ref file input (one file can't be a set)
@@ -366,7 +371,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 
 ## [2.2.2] - 2018-12-19
 
-### `Added`
+### Added - [2.2.2]
 
 - [#671](https://github.com/SciLifeLab/Sarek/pull/671) - New `publishDirMode` param and docs
 - [#673](https://github.com/SciLifeLab/Sarek/pull/673), [#675](https://github.com/SciLifeLab/Sarek/pull/675),  [#676](https://github.com/SciLifeLab/Sarek/pull/676) - Profiles for BinAC and CFC clusters in Tübingen
@@ -376,7 +381,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#698](https://github.com/SciLifeLab/Sarek/pull/698) - Add btb profile for munin server
 - [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Add `font-ttf-dejavu-sans-mono` `2.37` and `fontconfig` `2.12.6` to container
 
-### `Changed`
+### Changed - [2.2.2]
 
 - [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script
 - [#671](https://github.com/SciLifeLab/Sarek/pull/671) - `publishDir` modes are now params
@@ -390,7 +395,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#705](https://github.com/SciLifeLab/Sarek/pull/705) - Change `--TMP_DIR` by `--tmp-dir` for `GATK` `4.0.9.0` `BaseRecalibrator`
 - [#706](https://github.com/SciLifeLab/Sarek/pull/706) - Update `Travis CI` testing
 
-### `Fixed`
+### Fixed - [2.2.2]
 
 - [#665](https://github.com/SciLifeLab/Sarek/pull/665) - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the `MarkDuplicates` process, so metrics too
 - [#672](https://github.com/SciLifeLab/Sarek/pull/672) - Process `PullSingularityContainers` from `buildContainers.nf` now expect a file with the correct `.simg` extension for singularity images, and no longer the `.img` one.
@@ -401,13 +406,13 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 
 ## [2.2.1] - 2018-10-04
 
-### `Changed`
+### Changed - [2.2.1]
 
 - [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule
 - [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Update `Nextflow` to `0.32.0`
 - [#660](https://github.com/SciLifeLab/Sarek/pull/660) - Update docs
 
-### `Fixed`
+### Fixed - [2.2.1]
 
 - [#657](https://github.com/SciLifeLab/Sarek/pull/657) - Fix `RunMultiQC.nf` bug
 - [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Fix bugs due to updating `Nextflow`
@@ -416,7 +421,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 
 Skårki is one of the main massif in the Sarek National Park.
 
-### `Added`
+### Added - [2.2.0]
 
 - [#613](https://github.com/SciLifeLab/Sarek/pull/613) - Add Issue Templates (bug report and feature request)
 - [#614](https://github.com/SciLifeLab/Sarek/pull/614) - Add PR Template
@@ -428,7 +433,7 @@ Skårki is one of the main massif in the Sarek National Park.
 - [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Add a complete example analysis to docs
 - [#640](https://github.com/SciLifeLab/Sarek/pull/640), [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Add helper script for changing version number
 
-### `Changed`
+### Changed - [2.2.0]
 
 - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version
 - [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
@@ -448,13 +453,13 @@ Skårki is one of the main massif in the Sarek National Park.
 - [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `VCFanno` 0.2.8 -> 0.3.0
 - [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `VCFtools` 0.1.15 -> 0.1.16
 
-### `Removed`
+### Removed - [2.2.0]
 
 - [#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`
+### Fixed - [2.2.0]
 
 - [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix `VEP` tests
 - [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Fix links in MD files
@@ -463,7 +468,7 @@ Skårki is one of the main massif in the Sarek National Park.
 
 Ruotes is one of the main massif in the Sarek National Park.
 
-### `Added`
+### Added - [2.1.0]
 
 - [#555](https://github.com/SciLifeLab/Sarek/pull/555) - `snpEff` output into `VEP`
 - [#556](https://github.com/SciLifeLab/Sarek/pull/556) - `Strelka` Best Practices
@@ -482,7 +487,7 @@ Ruotes is one of the main massif in the Sarek National Park.
 - [#606](https://github.com/SciLifeLab/Sarek/pull/606) - Add test data as a submodule from [`Sarek-data`](https://github.com/SciLifeLab/Sarek-data)
 - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Add documentation on how to install Nextflow on `bianca`
 
-### `Changed`
+### Changed - [2.1.0]
 
 - [#557](https://github.com/SciLifeLab/Sarek/pull/557), [#583](https://github.com/SciLifeLab/Sarek/pull/583), [#585](https://github.com/SciLifeLab/Sarek/pull/585), [#588](https://github.com/SciLifeLab/Sarek/pull/588) - Update help
 - [#560](https://github.com/SciLifeLab/Sarek/pull/560) - `GitHub` langage for the repository is now `Nextflow`
@@ -503,7 +508,7 @@ Ruotes is one of the main massif in the Sarek National Park.
 - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG`
 - [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated `Nextflow ``$name` syntax with `withName`
 
-### `Fixed`
+### Fixed - [2.1.0]
 
 - [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`
 - [#566](https://github.com/SciLifeLab/Sarek/pull/566) - `slurmDownload` profile
@@ -512,7 +517,7 @@ Ruotes is one of the main massif in the Sarek National Park.
 - [#590](https://github.com/SciLifeLab/Sarek/pull/590), [#593](https://github.com/SciLifeLab/Sarek/pull/593) - Fix `Singularity` installation in `Travis CI` testing
 - [#598](https://github.com/SciLifeLab/Sarek/pull/598), [#601](https://github.com/SciLifeLab/Sarek/pull/601) - Fixes for  `Python` script `selectROI.py` to work with `CLC` viewer
 
-### `Removed`
+### Removed - [2.1.0]
 
 - [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Remove `Mutect1`
 
@@ -520,7 +525,7 @@ Ruotes is one of the main massif in the Sarek National Park.
 
 First release under the `Sarek` name, from the National Park in Northern Sweden
 
-### `Added`
+### Added - [2.0.0]
 
 - Basic wrapper script
 - Abstract, posters and figures
@@ -531,7 +536,7 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 - Some `runOptions` for `docker` (prevent some user right problem)
 - This `CHANGELOG`
 
-### `Changed`
+### Changed - [2.0.0]
 
 - `CAW` is now `Sarek`
 - Dissect Workflow in 5 new scripts: `annotate.nf`, `main.nf`, `germlineVC.nf`, `runMultiQC.nf` and `somaticVC.nf`
@@ -554,12 +559,12 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 - `nucleotidesPerSecond` is now `params.nucleotidesPerSecond`
 - Default `params.tag` is now `latest` instead of current version, so `--tag` needs to be specified with the right version to be sure of using the `containers` corresponding
 
-### `Deprecated`
+### Deprecated - [2.0.0]
 
 - `standard` profile
 - `uppmax-localhost.config` file
 
-### `Removed`
+### Removed - [2.0.0]
 
 - `scripts/skeleton_batch.sh`
 - Old data and tsv files
@@ -568,14 +573,14 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 - Some `runOptions` for `Singularity` (binding not needed anymore on `UPPMAX`)
 - `download` profile
 
-### `Fixed`
+### Fixed - [2.0.0]
 
 - [#530](https://github.com/SciLifeLab/Sarek/issues/530) - Use `$PWD` for default `outDir`
 - [#533](https://github.com/SciLifeLab/Sarek/issues/533) - Replace `VEP` `--pick` option by `--per_gene`
 
 ## [1.2.5] - 2018-01-18
 
-### `Added`
+### Added - [1.2.5]
 
 - `Zenodo` for DOI
 - Delivery README
@@ -588,7 +593,7 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 - `aws-batch.config` config file
 - `--noBAMQC` params (failing sometimes on `Bianca`)
 
-### `Changed`
+### Changed - [1.2.5]
 
 - Update `Nextflow` to `0.26.0` (new fancy report + `AWS Batch`)
 - Extra time on `Travis CI` testing
@@ -596,7 +601,7 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 - Update `MultiQC` to `1.3` (`MEGAQC` FTW)
 - Move and rename some test files
 
-### `Fixed`
+### Fixed - [1.2.5]
 
 - Version of `COSMIC` `GRCh37` `v83`
 - Write an error message when `--sampleDir` does not find any FASTQ files
@@ -605,7 +610,7 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 
 ## [1.2.4] - 2017-10-27
 
-### `Fixed`
+### Fixed - [1.2.4]
 
 - [#488](https://github.com/SciLifeLab/Sarek/issues/488) - Better CPU requirements for `ConcatVCF`
 - [#489](https://github.com/SciLifeLab/Sarek/issues/489) - Exception handling for `ASCAT`
@@ -613,7 +618,7 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 
 ## [1.2.3] - 2017-10-18
 
-### `Fixed`
+### Fixed - [1.2.3]
 
 - [#357](https://github.com/SciLifeLab/Sarek/issues/357) - `ASCAT` works for `GRCh38`
 - [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on `/scratch`
@@ -622,23 +627,23 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 
 ## [1.2.2] - 2017-10-06
 
-### `Fixed`
+### Fixed - [1.2.2]
 
 - [#479](https://github.com/SciLifeLab/Sarek/issues/479) - Typo in `uppmax-localhost.config`
 
 ## [1.2.1] - 2017-10-06
 
-### `Changed`
+### Changed - [1.2.1]
 
 - `runascat` and `runconvertallelecounts` containers are now replaced by `r-base`
 - `willmclaren/ensembl-vep:release_90.5` is now base for `vepgrch37` and `vepgrch38`
 
-### `Removed`
+### Removed - [1.2.1]
 
 - `vep` container
 - `strelka_config.ini` file
 
-### `Fixed`
+### Fixed - [1.2.1]
 
 - [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on /scratch
 - [#472](https://github.com/SciLifeLab/Sarek/issues/472) - Update function to check `Nextflow` version
@@ -646,30 +651,30 @@ First release under the `Sarek` name, from the National Park in Northern Sweden
 
 ## [1.2.0] - 2017-10-02
 
-### `Changed`
+### Changed - [1.2.0]
 
 - Fix version for Manuscript
 
 ## [1.1] - 2017-09-15
 
-### `Added`
+### Added - [1.1]
 
 - `Singularity` possibilities
 
-### `Changed`
+### Changed - [1.1]
 
 - Reports made by default
 - Intervals file can be a bed file
 - Normal sample preprocessing + `HaplotypeCaller` is possible
 - Better `Travis CI` tests
 
-### `Fixed`
+### Fixed - [1.1]
 
 - Memory requirements
 
 ## [1.0] - 2017-02-16
 
-### `Added`
+### Added - [1.0]
 
 - `Docker` possibilities
 

From 828a4b729b0e63d88bdee165afd1788711f18ebc Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 10:58:26 +0100
Subject: [PATCH 22/23] update rules for markdownlint

---
 .github/markdownlint.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
index dbff1a684a..51a4466a43 100644
--- a/.github/markdownlint.yml
+++ b/.github/markdownlint.yml
@@ -1,8 +1,6 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-duplicate-header:
-    siblings_only: true
 no-inline-html: 
     allowed_elements:
         - a

From 0b69b5c34f4ce03646b42f4cea9e05ecd8a3727b Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Fri, 27 Mar 2020 15:28:00 +0100
Subject: [PATCH 23/23] Apply suggestions from code review

Co-Authored-By: Gisela Gabernet <gisela.gabernet@gmail.com>
---
 conf/test_split_fastq.config | 4 ++--
 conf/test_targeted.config    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/test_split_fastq.config b/conf/test_split_fastq.config
index 73d1dfc1d4..d2e6595caf 100644
--- a/conf/test_split_fastq.config
+++ b/conf/test_split_fastq.config
@@ -4,11 +4,11 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_no_split_fastq
+ *   nextflow run nf-core/sarek -profile test_split_fastq
  */
 
 includeConfig 'test.config'
 
 params {
   split_fastq = 500
-}
\ No newline at end of file
+}
diff --git a/conf/test_targeted.config b/conf/test_targeted.config
index e39e9f91eb..9d3b38307e 100644
--- a/conf/test_targeted.config
+++ b/conf/test_targeted.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_no_split_fastq
+ *   nextflow run nf-core/sarek -profile test_targeted
  */
 
 includeConfig 'test.config'
@@ -12,4 +12,4 @@ includeConfig 'test.config'
 params {
   target_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/target.bed'
   tools = 'manta,strelka'
-}
\ No newline at end of file
+}