From 1b5f50e58e28bed626571e4f4182fae20b4a1639 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 10 Jan 2020 06:56:57 +0100
Subject: [PATCH 01/13] Removes GATK UG Downloading as not easily downloadable
 anymore with GATK wbesite update

---
 .github/workflows/nf-core_eager.yml | 18 +++++++-------
 .travis.yml                         |  6 ++---
 docs/usage.md                       |  6 ++++-
 main.nf                             | 37 +++++++++--------------------
 nextflow.config                     |  1 +
 5 files changed, 29 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 71eec1006..7213d06af 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -86,15 +86,15 @@ jobs:
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
-      - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
-      - name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-        run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
-      - name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
-        run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
+      #- name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
+      #  run: |
+      #    nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+      #- name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
+      #  run: |
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+      #- name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
+      #  run: |
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
diff --git a/.travis.yml b/.travis.yml
index b12effff7..eef48337b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -78,11 +78,11 @@ script:
   # SKIPPING: Test checking all skip steps work i.e. input bam, skipping straight to genotyping
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
   # VCF2GENOME: Test running GATK UnifiedGenotyper and run VCF2GENOME
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
   # BAM_INPUT: Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
   # BAM_INPUT: Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
diff --git a/docs/usage.md b/docs/usage.md
index 7e5103464..81a745208 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -713,12 +713,16 @@ Turns on genotyping to run on all post-dedup and downstream BAMs. For example if
 
 Specifies which genotyper to use. Current options are GATK (v3.5) UnifiedGenotyper or GATK (v4.xx). Furthermore, the FreeBayes Caller is available. Specify `'freebayes'`, `'hc'` or `'ug'` respectively.
 
-> NB that while UnifiedGenotyper is more suitable for low-coverage ancient DNA (HaplotypeCaller does _de novo_ assembly around each variant site), it is officially deperecated by the Broad Institute and is only accessible by an archived version not properly avaliable on `conda`. Therefore specifying 'ug' will download the GATK 3.5 `-jar` for you. This option therefore cannot be used when running the pipeline offline.
+> NB that while UnifiedGenotyper is more suitable for low-coverage ancient DNA (HaplotypeCaller does _de novo_ assembly around each variant site), it is officially deperecated by the Broad Institute and is only accessible by an archived version not properly avaliable on `conda`. Therefore if specifying 'ug', will need to supply a GATK 3.5 `-jar` to the parameter `gatk_ug_jar`. Note that this means the pipline is not fully reproducible in this configuration, unless you personally supply the `.jar` file.
 
 #### `--genotyping_source`
 
 Indicates which BAM file to use for genotyping, depending on what BAM processing modules you have turned on. Options are: `'raw'` for mapped only, filtered, or DeDup BAMs (with priority right to left); `'trimmed'` (for base clipped BAMs); `'pmd'` (for pmdtools output). Default is: `'raw'`.
 
+#### `--gatk_ug_jar`
+
+Specify a path to a local copy of a GATK 3.5 `.jar` file, preferably version '3.5-0-g36282e4'. The download location of this may be avaliable from the GATK forums of the Broad Institute.
+
 #### `--gatk_call_conf`
 
 If selected a GATK genotyper phred-scaled confidence threshold of a given SNP/INDEL call. Default: 30
diff --git a/main.nf b/main.nf
index 0530d2203..5cbca6de5 100644
--- a/main.nf
+++ b/main.nf
@@ -124,8 +124,9 @@ def helpMessage() {
 
     Genotyping
       --run_genotyping                Perform genotyping on deduplicated BAMs.
-      --genotyping_tool               Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller or Freebayes. Note: UnifiedGenotyper uses now deprecated GATK 3.5 and requires internet access. Options: 'ug', 'hc', 'freebayes'
+      --genotyping_tool               Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller or Freebayes. Note: UnifiedGenotyper requires user-supplied defined GATK 3.5 jar file. Options: 'ug', 'hc', 'freebayes'
       --genotyping_source             Specify which input BAM to use for genotyping. Options: 'raw', 'trimmed' or 'pmd' Default: 'raw'
+      --gatk_ug_jar                   When specifying to use GATK UnifiedGenotyper, path to GATK 3.5 .jar.
       --gatk_call_conf                Specify GATK phred-scaled confidence threshold. Default: 30.
       --gatk_ploidy                   Specify GATK organism ploidy. Default: 2.
       --gatk_dbsnp                    Specify VCF file for output VCF SNP annotation (Optional). Gzip not accepted.
@@ -360,6 +361,10 @@ if (params.run_genotyping){
   if (params.genotyping_tool != 'ug' && params.genotyping_tool != 'hc' && params.genotyping_tool != 'freebayes') {
   exit 1, "Please specify a genotyper. Options: 'ug', 'hc', 'freebayes'. You gave: ${params.genotyping_tool}!"
   }
+
+  if (params.genotyping_tool == 'ug' && params.gatk_ug_jar == '') {
+  exit 1, "Please specify path to a GATK 3.5 .jar file."
+  }
   
   if (params.gatk_ug_out_mode != 'EMIT_VARIANTS_ONLY' && params.gatk_ug_out_mode != 'EMIT_ALL_CONFIDENT_SITES' && params.gatk_ug_out_mode != 'EMIT_ALL_SITES') {
   exit 1, "Please check your GATK output mode. Options are: 'EMIT_VARIANTS_ONLY', 'EMIT_ALL_CONFIDENT_SITES', 'EMIT_ALL_SITES'. You gave: ${params.gatk_out_mode}!"
@@ -1685,33 +1690,13 @@ if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
 
 
 /*
- Step 12a: Genotyping - UnifiedGenotyper Downloading
- NB: GATK 3.5 is the last release with VCF output in "old" VCF format, not breaking downstream tools. Therefore we need it (for now at least until downstream tools can read proper 4.2 VCFs... )
-    
+ Step 12b: Genotyping - UG
+ NB: GATK 3.5 is the last release with VCF output in "old" VCF format, not breaking MVA. Therefore we need it (for now at least until downstream tools can read proper 4.2 VCFs... )
  */
 
-ch_gatk_download = Channel.value("download")
-
- process download_gatk_v3_5 {
-    label 'sc_tiny'
-    when: params.run_genotyping && params.genotyping_tool == 'ug'
-
-    input: 
-    val "download" from ch_gatk_download
-
-    output:
-    file "*.jar" into ch_unifiedgenotyper_jar,ch_unifiedgenotyper_versions_jar
-
-    """
-    wget -O GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 --referer https://software.broadinstitute.org/ 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.5-0-g36282e4' 
-    tar xjf GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 
-    """
-
- }
-
-/*
- Step 12b: Genotyping - UG
-*/
+Channel
+  .value(params.gatk_ug_jar)
+  .into{ ch_unifiedgenotyper_jar; ch_unifiedgenotyper_versions_jar }
 
  process genotyping_ug {
   label 'mc_small'
diff --git a/nextflow.config b/nextflow.config
index fb5879ce7..87c8635f1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -115,6 +115,7 @@ params {
   run_genotyping = false
   genotyping_tool = ''
   genotyping_source = "raw"
+  gatk_ug_jar = ''
   gatk_ug_genotype_model = 'SNP'
   gatk_hc_emitrefconf = 'GVCF'
   gatk_call_conf = '30'

From 1467b521ecff5f9d693c5c78e756e236703d5045 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 10 Jan 2020 08:22:33 +0100
Subject: [PATCH 02/13] Fixed access to manually supplied GATK 3.5 jar and
 improve docs

---
 docs/usage.md | 2 ++
 main.nf       | 9 +++------
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 81a745208..389d54133 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -723,6 +723,8 @@ Indicates which BAM file to use for genotyping, depending on what BAM processing
 
 Specify a path to a local copy of a GATK 3.5 `.jar` file, preferably version '3.5-0-g36282e4'. The download location of this may be avaliable from the GATK forums of the Broad Institute.
 
+> You must manually report your version of GATK 3.5 in publications/MultiQC as it is not included in our container.
+
 #### `--gatk_call_conf`
 
 If selected a GATK genotyper phred-scaled confidence threshold of a given SNP/INDEL call. Default: 30
diff --git a/main.nf b/main.nf
index 5cbca6de5..dd42d3181 100644
--- a/main.nf
+++ b/main.nf
@@ -363,7 +363,7 @@ if (params.run_genotyping){
   }
 
   if (params.genotyping_tool == 'ug' && params.gatk_ug_jar == '') {
-  exit 1, "Please specify path to a GATK 3.5 .jar file."
+  exit 1, "Please specify path to a GATK 3.5 .jar file with --gatk_ug_jar."
   }
   
   if (params.gatk_ug_out_mode != 'EMIT_VARIANTS_ONLY' && params.gatk_ug_out_mode != 'EMIT_ALL_CONFIDENT_SITES' && params.gatk_ug_out_mode != 'EMIT_ALL_SITES') {
@@ -1695,8 +1695,8 @@ if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
  */
 
 Channel
-  .value(params.gatk_ug_jar)
-  .into{ ch_unifiedgenotyper_jar; ch_unifiedgenotyper_versions_jar }
+  .fromPath( params.gatk_ug_jar )
+  .set{ ch_unifiedgenotyper_jar }
 
  process genotyping_ug {
   label 'mc_small'
@@ -2175,9 +2175,6 @@ process get_software_versions {
     mtnucratio --help &> v_mtnucratiocalculator.txt || true
     sexdeterrmine --version &> v_sexdeterrmine.txt || true
 
-    ## Hardcoded as no --version flag or equivalent
-    echo 'version 3.5-0-g36282e4' > v_gatk3_5.txt
-
     scrape_software_versions.py &> software_versions_mqc.yaml
     """
 }

From 3b5ca4d401775202c192794de284e5cb4a8396ff Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 10 Jan 2020 08:35:03 +0100
Subject: [PATCH 03/13] Fixed channel creation when not running UG

---
 main.nf | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index dd42d3181..95b5fed18 100644
--- a/main.nf
+++ b/main.nf
@@ -1694,9 +1694,16 @@ if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
  NB: GATK 3.5 is the last release with VCF output in "old" VCF format, not breaking MVA. Therefore we need it (for now at least until downstream tools can read proper 4.2 VCFs... )
  */
 
-Channel
-  .fromPath( params.gatk_ug_jar )
-  .set{ ch_unifiedgenotyper_jar }
+if ( params.gatk_ug_jar != '' ) {
+  Channel
+    .fromPath( params.gatk_ug_jar )
+    .set{ ch_unifiedgenotyper_jar }
+} else {
+  Channel
+    .empty()
+    .set{ ch_unifiedgenotyper_jar }
+}
+
 
  process genotyping_ug {
   label 'mc_small'

From 67497de8c62a7c764f4d7f0c1f9a9464560e4756 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 10 Jan 2020 10:20:03 +0100
Subject: [PATCH 04/13] Remove gatk 3.5 version entry in
 scrap_software_versions.py

---
 bin/scrape_software_versions.py |  4 +--
 main.nf                         | 52 ++++++++++++++++-----------------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
index f03211b40..a6114aacb 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -15,7 +15,7 @@
     'BWA': ['v_bwa.txt', r"Version: (\S+)"],
     'Qualimap': ['v_qualimap.txt', r"QualiMap v.(\S+)"],
     'GATK HaplotypeCaller': ['v_gatk.txt', r" v(\S+)"],
-    'GATK UnifiedGenotyper': ['v_gatk3_5.txt', r"version (\S+)"],
+    #'GATK UnifiedGenotyper': ['v_gatk3_5.txt', r"version (\S+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: (\S+);"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],
     'DamageProfiler' : ['v_damageprofiler.txt', r"DamageProfiler v(\S+)"],
@@ -47,7 +47,7 @@
 results['Qualimap'] = '<span style="color:#999999;\">N/A</span>'
 results['Preseq'] = '<span style="color:#999999;\">N/A</span>'
 results['GATK HaplotypeCaller'] = '<span style="color:#999999;\">N/A</span>'
-results['GATK UnifiedGenotyper'] = '<span style="color:#999999;\">N/A</span>'
+#results['GATK UnifiedGenotyper'] = '<span style="color:#999999;\">N/A</span>'
 results['freebayes'] = '<span style="color:#999999;\">N/A</span>'
 results['VCF2genome'] = '<span style="color:#999999;\">N/A</span>'
 results['MTNucRatioCalculator'] = '<span style="color:#999999;\">N/A</span>'
diff --git a/main.nf b/main.nf
index 95b5fed18..da443b806 100644
--- a/main.nf
+++ b/main.nf
@@ -2155,32 +2155,32 @@ process get_software_versions {
 
     script:
     """
-    echo $workflow.manifest.version &> v_pipeline.txt
-    echo $workflow.nextflow.version &> v_nextflow.txt
-    fastqc --version &> v_fastqc.txt 2>&1 || true
-    AdapterRemoval --version  &> v_adapterremoval.txt 2>&1 || true
-    fastp --version &> v_fastp.txt 2>&1 || true
-    bwa &> v_bwa.txt 2>&1 || true
-    circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
-    samtools --version &> v_samtools.txt 2>&1 || true
-    dedup -v &> v_dedup.txt 2>&1 || true
-    picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
-    qualimap --version &> v_qualimap.txt 2>&1 || true
-    preseq &> v_preseq.txt 2>&1 || true
-    gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
-    freebayes --version &> v_freebayes.txt 2>&1 || true
-    bedtools --version &> v_bedtools.txt 2>&1 || true
-    damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
-    bam --version &> v_bamutil.txt 2>&1 || true
-    pmdtools --version &> v_pmdtools.txt 2>&1 || true
-    angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true 
-    multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
-    malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
-    MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
-    multiqc --version &> v_multiqc.txt 2>&1 || true
-    vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
-    mtnucratio --help &> v_mtnucratiocalculator.txt || true
-    sexdeterrmine --version &> v_sexdeterrmine.txt || true
+    echo "eager" && echo $workflow.manifest.version &> v_pipeline.txt
+    echo "nf" && echo $workflow.nextflow.version &> v_nextflow.txt
+    echo "fqc" && fastqc --version &> v_fastqc.txt 2>&1 || true
+    echo "ar" && AdapterRemoval --version  &> v_adapterremoval.txt 2>&1 || true
+    echo "fp" && fastp --version &> v_fastp.txt 2>&1 || true
+    echo "bwa" && bwa &> v_bwa.txt 2>&1 || true
+    echo "cg" && circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
+    echo "st" && samtools --version &> v_samtools.txt 2>&1 || true
+    echo "dd" && dedup -v &> v_dedup.txt 2>&1 || true
+    echo "pc" && picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
+    echo "qm" && qualimap --version &> v_qualimap.txt 2>&1 || true
+    echo "pr" && preseq &> v_preseq.txt 2>&1 || true
+    echo "gk" && gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
+    echo "fb" && freebayes --version &> v_freebayes.txt 2>&1 || true
+    echo "bt" && bedtools --version &> v_bedtools.txt 2>&1 || true
+    echo "dp" && damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
+    echo "bu" && bam --version &> v_bamutil.txt 2>&1 || true
+    echo "pd" && pmdtools --version &> v_pmdtools.txt 2>&1 || true
+    echo "ad" && angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true 
+    echo "ma" && multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
+    echo "mt" && malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
+    echo "me" && MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
+    echo "mq" && multiqc --version &> v_multiqc.txt 2>&1 || true
+    echo "vg" && vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
+    echo "mn" && mtnucratio --help &> v_mtnucratiocalculator.txt || true
+    echo "sd" && sexdeterrmine --version &> v_sexdeterrmine.txt || true
 
     scrape_software_versions.py &> software_versions_mqc.yaml
     """

From baa2210ad040566132c977af2500078307c74253 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Fri, 10 Jan 2020 11:20:54 +0100
Subject: [PATCH 05/13] Removed debugging prints

---
 main.nf | 52 ++++++++++++++++++++++++++--------------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/main.nf b/main.nf
index da443b806..95b5fed18 100644
--- a/main.nf
+++ b/main.nf
@@ -2155,32 +2155,32 @@ process get_software_versions {
 
     script:
     """
-    echo "eager" && echo $workflow.manifest.version &> v_pipeline.txt
-    echo "nf" && echo $workflow.nextflow.version &> v_nextflow.txt
-    echo "fqc" && fastqc --version &> v_fastqc.txt 2>&1 || true
-    echo "ar" && AdapterRemoval --version  &> v_adapterremoval.txt 2>&1 || true
-    echo "fp" && fastp --version &> v_fastp.txt 2>&1 || true
-    echo "bwa" && bwa &> v_bwa.txt 2>&1 || true
-    echo "cg" && circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
-    echo "st" && samtools --version &> v_samtools.txt 2>&1 || true
-    echo "dd" && dedup -v &> v_dedup.txt 2>&1 || true
-    echo "pc" && picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
-    echo "qm" && qualimap --version &> v_qualimap.txt 2>&1 || true
-    echo "pr" && preseq &> v_preseq.txt 2>&1 || true
-    echo "gk" && gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
-    echo "fb" && freebayes --version &> v_freebayes.txt 2>&1 || true
-    echo "bt" && bedtools --version &> v_bedtools.txt 2>&1 || true
-    echo "dp" && damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
-    echo "bu" && bam --version &> v_bamutil.txt 2>&1 || true
-    echo "pd" && pmdtools --version &> v_pmdtools.txt 2>&1 || true
-    echo "ad" && angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true 
-    echo "ma" && multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
-    echo "mt" && malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
-    echo "me" && MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
-    echo "mq" && multiqc --version &> v_multiqc.txt 2>&1 || true
-    echo "vg" && vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
-    echo "mn" && mtnucratio --help &> v_mtnucratiocalculator.txt || true
-    echo "sd" && sexdeterrmine --version &> v_sexdeterrmine.txt || true
+    echo $workflow.manifest.version &> v_pipeline.txt
+    echo $workflow.nextflow.version &> v_nextflow.txt
+    fastqc --version &> v_fastqc.txt 2>&1 || true
+    AdapterRemoval --version  &> v_adapterremoval.txt 2>&1 || true
+    fastp --version &> v_fastp.txt 2>&1 || true
+    bwa &> v_bwa.txt 2>&1 || true
+    circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
+    samtools --version &> v_samtools.txt 2>&1 || true
+    dedup -v &> v_dedup.txt 2>&1 || true
+    picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
+    qualimap --version &> v_qualimap.txt 2>&1 || true
+    preseq &> v_preseq.txt 2>&1 || true
+    gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
+    freebayes --version &> v_freebayes.txt 2>&1 || true
+    bedtools --version &> v_bedtools.txt 2>&1 || true
+    damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
+    bam --version &> v_bamutil.txt 2>&1 || true
+    pmdtools --version &> v_pmdtools.txt 2>&1 || true
+    angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true 
+    multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
+    malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
+    MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
+    multiqc --version &> v_multiqc.txt 2>&1 || true
+    vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
+    mtnucratio --help &> v_mtnucratiocalculator.txt || true
+    sexdeterrmine --version &> v_sexdeterrmine.txt || true
 
     scrape_software_versions.py &> software_versions_mqc.yaml
     """

From 1cd8e4e8b38aaa84c0207df903cb8263e00d9837 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 06:23:06 +0100
Subject: [PATCH 06/13] Re-enabled GATK UG tests with new download location
 performed outside EAGER

---
 .github/workflows/nf-core_eager.yml | 21 ++++++++++++---------
 .travis.yml                         | 16 ++++++++--------
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 7213d06af..14b057a12 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -86,15 +86,9 @@ jobs:
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
-      #- name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-      #  run: |
-      #    nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
-      #- name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-      #  run: |
-      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
-      #- name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
-      #  run: |
-      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
+      - name: GENOTYPING_UG Download GATK UG 3.5 jar
+        run : |
+          mkdir -p jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
@@ -125,3 +119,12 @@ jobs:
       - name: MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
+      - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+      - name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
+        run: |
+         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+      - name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
+        run: |
+         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
diff --git a/.travis.yml b/.travis.yml
index eef48337b..a19e8f403 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -77,12 +77,6 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-freebayes" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes'
   # SKIPPING: Test checking all skip steps work i.e. input bam, skipping straight to genotyping
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
-  # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
-  # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
-  # VCF2GENOME: Test running GATK UnifiedGenotyper and run VCF2GENOME
-  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
   # BAM_INPUT: Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
   # BAM_INPUT: Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
@@ -99,5 +93,11 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-nuclearcontamination" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_nuclear_contamination
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
-
-
+  # Download GATK 3.5 JAR
+  - mkdir -p ${TRAVIS_BUILD_DIR}/jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+  # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+  # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+  # VCF2GENOME: Test running GATK UnifiedGenotyper and run VCF2GENOME
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome

From 7afe4a1eed6a2a2cebe7e4938bce39c6fc2241fa Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 06:46:03 +0100
Subject: [PATCH 07/13] Missed a &&

---
 .github/workflows/nf-core_eager.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 14b057a12..5b75251e3 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -86,9 +86,6 @@ jobs:
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
-      - name: GENOTYPING_UG Download GATK UG 3.5 jar
-        run : |
-          mkdir -p jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
@@ -119,6 +116,9 @@ jobs:
       - name: MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
+      - name: GENOTYPING_UG Download GATK UG 3.5 jar
+        run : |
+          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer

From 3994a1b409ff4356988b489529f2fe5910b60340 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 07:15:50 +0100
Subject: [PATCH 08/13] Don't code at 5am. Fix capital and travis missing &&

---
 .github/workflows/nf-core_eager.yml | 2 +-
 .travis.yml                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 5b75251e3..fe9a701f4 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -118,7 +118,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: GENOTYPING_UG Download GATK UG 3.5 jar
         run : |
-          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
diff --git a/.travis.yml b/.travis.yml
index a19e8f403..ac178c43b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -94,7 +94,7 @@ script:
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
   # Download GATK 3.5 JAR
-  - mkdir -p ${TRAVIS_BUILD_DIR}/jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS

From 5c77efa3cdf8da93b5f1cfdc49a2cf2be362305b Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 08:18:55 +0100
Subject: [PATCH 09/13] Try to find where JAR is

---
 .github/workflows/nf-core_eager.yml | 2 +-
 .travis.yml                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index fe9a701f4..0e2efa4f3 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -118,7 +118,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: GENOTYPING_UG Download GATK UG 3.5 jar
         run : |
-          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 && && readlink -f jars/GenomeAnalysisTK.jar
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
diff --git a/.travis.yml b/.travis.yml
index ac178c43b..2827d17e6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -94,7 +94,7 @@ script:
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
   # Download GATK 3.5 JAR
-  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 && readlink -f ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar 
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS

From 22d03f4d95b339faa66ab1d561670a1ecf3d5d47 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 09:12:01 +0100
Subject: [PATCH 10/13] Revert "Try to find where JAR is"

This reverts commit 5c77efa3cdf8da93b5f1cfdc49a2cf2be362305b.
---
 .github/workflows/nf-core_eager.yml | 2 +-
 .travis.yml                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 0e2efa4f3..fe9a701f4 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -118,7 +118,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: GENOTYPING_UG Download GATK UG 3.5 jar
         run : |
-          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 && && readlink -f jars/GenomeAnalysisTK.jar
+          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
diff --git a/.travis.yml b/.travis.yml
index 2827d17e6..ac178c43b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -94,7 +94,7 @@ script:
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
   # Download GATK 3.5 JAR
-  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 && readlink -f ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar 
+  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS

From 4381d6dfc66b3c3bc774908ab39f3f2f8e3ae0d7 Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 09:12:21 +0100
Subject: [PATCH 11/13] Revert "Don't code at 5am. Fix capital and travis
 missing &&"

This reverts commit 3994a1b409ff4356988b489529f2fe5910b60340.
---
 .github/workflows/nf-core_eager.yml | 2 +-
 .travis.yml                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index fe9a701f4..5b75251e3 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -118,7 +118,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: GENOTYPING_UG Download GATK UG 3.5 jar
         run : |
-          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/ && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
diff --git a/.travis.yml b/.travis.yml
index ac178c43b..a19e8f403 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -94,7 +94,7 @@ script:
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
   # Download GATK 3.5 JAR
-  - mkdir -p ${TRAVIS_BUILD_DIR}/jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+  - mkdir -p ${TRAVIS_BUILD_DIR}/jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS

From a05a792dc966b05c24f73d574d0ea8ed876cb7ff Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 09:12:36 +0100
Subject: [PATCH 12/13] Revert "Missed a &&"

This reverts commit 7afe4a1eed6a2a2cebe7e4938bce39c6fc2241fa.
---
 .github/workflows/nf-core_eager.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 5b75251e3..14b057a12 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -86,6 +86,9 @@ jobs:
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
+      - name: GENOTYPING_UG Download GATK UG 3.5 jar
+        run : |
+          mkdir -p jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
@@ -116,9 +119,6 @@ jobs:
       - name: MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
-      - name: GENOTYPING_UG Download GATK UG 3.5 jar
-        run : |
-          mkdir -p jars && wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
       - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer

From 44acd9bca091561631a5ab423f2fedd274f37b5f Mon Sep 17 00:00:00 2001
From: jfy133 <jfy133@gmail.com>
Date: Wed, 15 Jan 2020 09:12:54 +0100
Subject: [PATCH 13/13] Revert "Re-enabled GATK UG tests with new download
 location performed outside EAGER"

This reverts commit 1cd8e4e8b38aaa84c0207df903cb8263e00d9837.
---
 .github/workflows/nf-core_eager.yml | 21 +++++++++------------
 .travis.yml                         | 16 ++++++++--------
 2 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/nf-core_eager.yml
index 14b057a12..7213d06af 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/nf-core_eager.yml
@@ -86,9 +86,15 @@ jobs:
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
-      - name: GENOTYPING_UG Download GATK UG 3.5 jar
-        run : |
-          mkdir -p jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p jars && tar xjf jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
+      #- name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
+      #  run: |
+      #    nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+      #- name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
+      #  run: |
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+      #- name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
+      #  run: |
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
@@ -119,12 +125,3 @@ jobs:
       - name: MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
         run: |
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
-      - name: TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
-      - name: GENOTYPING_UG/PMD/MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-        run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
-      - name: VCF2Genome Run basic pipeline with GATK unifiedgenotyper and run VCF2Genome
-        run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '/home/runner/work/eager/eager/jars/GenomeAnalysisTK.jar' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
diff --git a/.travis.yml b/.travis.yml
index a19e8f403..eef48337b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -77,6 +77,12 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-freebayes" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes'
   # SKIPPING: Test checking all skip steps work i.e. input bam, skipping straight to genotyping
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
+  # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+  # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+  # VCF2GENOME: Test running GATK UnifiedGenotyper and run VCF2GENOME
+  #- nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
   # BAM_INPUT: Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
   - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
   # BAM_INPUT: Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
@@ -93,11 +99,5 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-nuclearcontamination" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_nuclear_contamination
   # MTNUCRATIO Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nmtnucratio
   - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_mtnucratio
-  # Download GATK 3.5 JAR
-  - mkdir -p ${TRAVIS_BUILD_DIR}/jars wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -p ${TRAVIS_BUILD_DIR}/jars && tar xjf ${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2
-  # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
-  # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
-  # VCF2GENOME: Test running GATK UnifiedGenotyper and run VCF2GENOME
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-vcf2genome" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_ug_jar '${TRAVIS_BUILD_DIR}/jars/GenomeAnalysisTK.jar' --genotyping_source 'raw' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_vcf2genome
+
+