nf-core · apeltzer · Nov 17, 2020 · Nov 13, 2020 · Nov 13, 2020 · Nov 13, 2020
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,9 +26,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
+        uses: technote-space/get-diff-action@v4
         with:
-          PREFIX_FILTER: |
+          FILES: |
             Dockerfile
             environment.yml
 
@@ -142,22 +142,15 @@ jobs:
       - name: PMDTOOLS Test PMDtools works alone
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools
-      - name: GATK 3.5 Download resource files
-        run: |
-            mkdir -p jars/gatk_3_5
-            wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -P jars/gatk_3_5
-            tar xvf jars/gatk_3_5/GenomeAnalysisTK-3.5-0-g36282e4.tar.bz2 -C jars/gatk_3_5/
-            chmod +x jars/gatk_3_5/GenomeAnalysisTK.jar
-            GATK_JAR=$(readlink -f jars/gatk_3_5/GenomeAnalysisTK.jar)
       - name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --gatk_ug_jar '/home/runner/work/eager/eager/jars/gatk_3_5/GenomeAnalysisTK.jar' --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
+         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --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: COMPLEX LANE/LIBRARY MERGING Test running lane and library merging prior to GATK UnifiedGenotyper and running MultiVCFAnalyzer
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --gatk_ug_jar '/home/runner/work/eager/eager/jars/gatk_3_5/GenomeAnalysisTK.jar' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
       - name: GENOTYPING_UG ON TRIMMED BAM Test
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --gatk_ug_jar '/home/runner/work/eager/eager/jars/gatk_3_5/GenomeAnalysisTK.jar' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
+         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [2.3.0dev] - Wangen - Unreleased
+## [2.2.2dev] - Unreleased
 
 ### `Added`
 
@@ -13,8 +13,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Fixed AWS full test profile.
 - [#587](https://github.com/nf-core/eager/issues/587) - Re-implemented AdapterRemovalFixPrefix for DeDup compatibility of including singletons
+- [#602](https://github.com/nf-core/eager/issues/602) - Added the newly avaliable GATK 3.5 conda package.
 - [#610](https://github.com/nf-core/eager/issues/610) - Create bwa_index channel when specifying circularmapper as mapper
 
+### `Deprecated`
+
+- Flag `--gatk_ug_jar` has now been removed as GATK 3.5 is now avaliable within the nf-core/eager software environment.
+
 ## [2.2.1] - 2020-10-20
 
 ### `Fixed`

diff --git a/Dockerfile b/Dockerfile
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.3.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.2.2dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.0dev > nf-core-eager-2.3.0dev.yml
+RUN conda env export --name nf-core-eager-2.2.2dev > nf-core-eager-2.2.2dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

diff --git a/docs/usage.md b/docs/usage.md
@@ -1556,12 +1556,8 @@ UnifiedGenotyper or GATK Haplotype Caller (v4); and the FreeBayes Caller.
 Specify 'ug', 'hc', 'freebayes', 'pileupcaller' and 'angsd' respectively.
 
 > Note that while UnifiedGenotyper is more suitable for low-coverage ancient DNA
-> (HaplotypeCaller does _de novo_ assembly around each variant site), it is
-> officially deprecated by the Broad Institute and is only accessible by an
-> archived version not properly available 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 pipeline is not fully reproducible in this
-> configuration, unless you personally supply the `.jar` file.
+> (HaplotypeCaller does _de novo_ assembly around each variant site), be aware
+> GATK 3.5 it is officially deprecated by the Broad Institute.
 
 #### `--genotyping_source`
 
@@ -1570,17 +1566,6 @@ 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 available from the GATK
-forums or the [Google Cloud
-Storage](https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false)
-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, specify a GATK genotyper phred-scaled confidence threshold of a
@@ -4139,10 +4124,7 @@ Prior setting up the nf-core/eager run, we will need:
 3. A GFF file of gene sequence annotations (normally supplied with reference
    genomes downloaded from NCBI Genomes, in this context from
    [here](https://www.ncbi.nlm.nih.gov/genome/?term=Yersinia+pestis))
-4. The JAR file for GATK v3.5 downloadable from
-   [here](https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false)
-   (Make sure to extract the Zip file first!)
-5. [Optional] Previously made VCF GATK 3.5 files (see below for settings), of
+4. [Optional] Previously made VCF GATK 3.5 files (see below for settings), of
    previously published _Y. pestis_ genomes.
 
 We should also ensure we have the very latest version of the nf-core/eager
@@ -4474,7 +4456,7 @@ environmental relatives or other contaminants.
 
 For this we need to run genotyping, but specifically with GATK UnifiedGenotyper
 3.5 (as MultiVCFAnalyzer requires this particular format of VCF files). We will
-therefore turn on Genotyping, supply the path to the GATK 3.5 JAR file, and
+therefore turn on Genotyping, and
 check ploidy is set 2 so 'heterozygous' positions can be reported. We will also
 need to specify that we want to use the trimmed bams from the previous step.
 
@@ -4507,7 +4489,6 @@ nextflow run nf-core/eager \
 --run_genotyping \
 --genotyping_tool 'ug' \
 --genotyping_source 'trimmed' \
---gatk_ug_jar '../bin/GenomeAnalysisTK.jar' \
 --gatk_ploidy 2 \
 --gatk_ug_mode 'EMIT_ALL_SITES' \
 --gatk_ug_genotype_model 'SNP' \
@@ -4551,7 +4532,6 @@ nextflow run nf-core/eager \
 --run_genotyping \
 --genotyping_tool 'ug' \
 --genotyping_source 'trimmed' \
---gatk_ug_jar '../bin/GenomeAnalysisTK.jar' \
 --gatk_ploidy 2 \
 --gatk_ug_mode 'EMIT_ALL_SITES' \
 --gatk_ug_genotype_model 'SNP' \

diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,4 @@
-name: nf-core-eager-2.3.0dev
+name: nf-core-eager-2.2.2dev
 channels:
   - conda-forge
   - bioconda
@@ -20,6 +20,7 @@ dependencies:
   - bioconda::angsd=0.933
   - bioconda::circularmapper=1.93.5
   - bioconda::gatk4=4.1.7.0
+  - bioconda::gatk=3.5
   - bioconda::qualimap=2.2.2d
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.9

diff --git a/main.nf b/main.nf
@@ -136,9 +136,8 @@ def helpMessage() {
 
     Genotyping
       --run_genotyping [bool]                Turn on genotyping of BAM files.
-      --genotyping_tool [str]                Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller, Freebayes, or pileupCaller. Note: UnifiedGenotyper requires user-supplied defined GATK 3.5 jar file. Options: 'ug', 'hc', 'freebayes', 'pileupcaller', 'angsd'.
+      --genotyping_tool [str]                Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller, Freebayes, or pileupCaller. Options: 'ug', 'hc', 'freebayes', 'pileupcaller', 'angsd'.
       --genotyping_source [str]              Specify which input BAM to use for genotyping. Options: 'raw', 'trimmed' or 'pmd'. Default: '${params.genotyping_source}'
-      --gatk_ug_jar [file]                   When specifying to use GATK UnifiedGenotyper, path to GATK 3.5 .jar.
       --gatk_call_conf [num]                 Specify GATK phred-scaled confidence threshold. Default: ${params.gatk_call_conf}
       --gatk_ploidy [num]                    Specify GATK organism ploidy. Default: ${params.gatk_ploidy}
       --gatk_downsample [num]                Maximum depth coverage allowed for genotyping before down-sampling is turned on. Default: ${params.gatk_downsample}
@@ -416,14 +415,6 @@ if (params.run_genotyping){
   if (params.genotyping_tool != 'ug' && params.genotyping_tool != 'hc' && params.genotyping_tool != 'freebayes' && params.genotyping_tool != 'pileupcaller' && params.genotyping_tool != 'angsd' ) {
   exit 1, "[nf-core/eager] error: please specify a genotyper. Options: 'ug', 'hc', 'freebayes', 'pileupcaller'. Found parameter: --genotyping_tool '${params.genotyping_tool}'."
   }
-
-  if (params.genotyping_tool == 'ug' && params.gatk_ug_jar == '') {
-  exit 1, "[nf-core/eager] error: please specify path to a GATK 3.5 .jar file with --gatk_ug_jar."
-  }
-
-  if (params.genotyping_tool == 'ug' && !params.gatk_ug_jar.endsWith('.jar') ) {
-    exit 1, "[nf-core/eager] error: please specify path with --gatk_ug_jar to a valid GATK 3.5 binary that ends with .jar!. Found parameter: --gatk_ug_jar '${params.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') {
   exit 1, "[nf-core/eager] error: please check your GATK output mode. Options are: 'EMIT_VARIANTS_ONLY', 'EMIT_ALL_CONFIDENT_SITES', 'EMIT_ALL_SITES'. Found parameter: --gatk_ug_out_mode '${params.gatk_out_mode}'."
@@ -470,17 +461,6 @@ if (params.run_genotyping){
   }
 }
 
-// check manually supplied UG JAR found
-if ( params.gatk_ug_jar != '' ) {
-  Channel
-    .fromPath( params.gatk_ug_jar, checkIfExists: true )
-    .set{ ch_unifiedgenotyper_jar }
-} else {
-  Channel
-    .empty()
-    .set{ ch_unifiedgenotyper_jar }
-}
-
  // pileupCaller channel generation and input checks for 'random sampling' genotyping
 if (params.pileupcaller_bedfile.isEmpty()) {
   ch_bed_for_pileupcaller = Channel.fromPath("$baseDir/assets/nf-core_eager_dummy.txt")
@@ -2516,7 +2496,6 @@ process genotyping_ug {
   input:
   tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_damagemanipulation_for_genotyping_ug
   file fasta from ch_fasta_for_genotyping_ug.collect()
-  file jar from ch_unifiedgenotyper_jar.collect()
   file fai from ch_fai_for_ug.collect()
   file dict from ch_dict_for_ug.collect()
 
@@ -2530,9 +2509,9 @@ process genotyping_ug {
   if (params.gatk_dbsnp == '')
     """
     samtools index -b ${bam}
-    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
-    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
-    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
+    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
+    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
+    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
 
     $keep_realign
 
@@ -2541,9 +2520,9 @@ process genotyping_ug {
   else if (params.gatk_dbsnp != '')
     """
     samtools index ${bam}
-    java -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
-    java -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
-    java -jar ${jar} -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
+    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
+    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
+    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
 
     $keep_realign
 

diff --git a/nextflow.config b/nextflow.config
@@ -128,7 +128,6 @@ params {
   genotyping_tool = ''
   genotyping_source = 'raw'
   // gatk options
-  gatk_ug_jar = ''
   gatk_call_conf = 30
   gatk_ploidy = 2
   gatk_downsample = 250
@@ -338,7 +337,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.04.0'
-  version = '2.3.0dev'
+  version = '2.2.2dev'
 }
 
 // Function to ensure that resource requirements don't go beyond

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -877,9 +877,9 @@
                 },
                 "genotyping_tool": {
                     "type": "string",
-                    "description": "Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller, Freebayes, or pileupCaller. Note: UnifiedGenotyper requires user-supplied defined GATK 3.5 jar file. Options: 'ug', 'hc', 'freebayes', 'pileupcaller', 'angsd'.",
+                    "description": "Specify which genotyper to use either GATK UnifiedGenotyper, GATK HaplotypeCaller, Freebayes, or pileupCaller. Options: 'ug', 'hc', 'freebayes', 'pileupcaller', 'angsd'.",
                     "fa_icon": "fas fa-tools",
-                    "help_text": "Specifies which genotyper to use. Current options are: GATK (v3.5) UnifiedGenotyper or GATK Haplotype Caller (v4); and the FreeBayes Caller. Specify 'ug', 'hc', 'freebayes', 'pileupcaller' and 'angsd' respectively.\n\n> Note that while UnifiedGenotyper is more suitable for low-coverage ancient DNA (HaplotypeCaller does _de novo_ assembly around each variant site), it is officially deprecated by the Broad Institute and is only accessible by an archived version not properly available 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.",
+                    "help_text": "Specifies which genotyper to use. Current options are: GATK (v3.5) UnifiedGenotyper or GATK Haplotype Caller (v4); and the FreeBayes Caller. Specify 'ug', 'hc', 'freebayes', 'pileupcaller' and 'angsd' respectively.\n\n> > Note that while UnifiedGenotyper is more suitable for low-coverage ancient DNA (HaplotypeCaller does _de novo_ assembly around each variant site), be aware GATK 3.5 it is officially deprecated by the Broad Institute.",
                     "enum": [
                         "ug",
                         "hc",
@@ -895,12 +895,6 @@
                     "fa_icon": "fas fa-faucet",
                     "help_text": "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'`.\n"
                 },
-                "gatk_ug_jar": {
-                    "type": "string",
-                    "description": "When specifying to use GATK UnifiedGenotyper, path to GATK 3.5 .jar.",
-                    "fa_icon": "fas fa-archive",
-                    "help_text": "Specify a path to a local copy of a GATK 3.5 `.jar` file, preferably version\n'3.5-0-g36282e4'. The download location of this may be available from the GATK\nforums or the [Google Cloud\nStorage](https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false)\nof the Broad Institute."
-                },
                 "gatk_call_conf": {
                     "type": "integer",
                     "default": 30,