diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 75e282d9b..2aecd2e65 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -12,6 +12,7 @@ jobs:
       # PRs are only ok if coming from an nf-core dev branch
       - name: Check PRs
         run: |
+          { [[ $(git remote get-url origin) == *nf-core/eager ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
           echo "HOME: ${HOME}"
           echo "GITHUB_WORKFLOW: ${GITHUB_WORKFLOW}"
           echo "GITHUB_ACTION: ${GITHUB_ACTION}"
diff --git a/.github/workflows/nf-core_eager.yml b/.github/workflows/ci.yml
similarity index 65%
rename from .github/workflows/nf-core_eager.yml
rename to .github/workflows/ci.yml
index 7213d06af..9d02288b4 100644
--- a/.github/workflows/nf-core_eager.yml
+++ b/.github/workflows/ci.yml
@@ -10,20 +10,26 @@ jobs:
       - name: Try Creating Conda env
         run: |
           conda env create --prefix nf-core-eager-2.1.0dev-d95a13feb408cc17e95d38f16a81010d --file environment.yml
-  github_actions_ci:
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ubuntu-18.04
     env:
       TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
       NXF_ANSI_LOG: 0
     strategy:
       matrix:
-        endedness: ['--singleEnd', '--pairedEnd']
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+        endedness: ['--single_end', '--paired_end']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
         run: |
+          export NXF_VER=${{ matrix.nxf_ver }}
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+      - name: Download image
+        run: |
+          docker pull nfcore/eager:dev && docker tag nfcore/eager:dev nfcore/eager:dev
       - name: Extract branch name
         shell: bash
         run: echo "::set-env name=RUN_NAME::`echo ${GITHUB_REPOSITORY//\//_}`-`echo ${GITHUB_HEAD_REF//\//@} | rev | cut -f1 -d@ | rev`-${{ github.event_name }}-`echo ${GITHUB_SHA} | cut -c1-6`"
@@ -40,61 +46,61 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-preindex_ref" -profile test,docker ${{ matrix.endedness }} --bwa_index 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' 
       - name: REFERENCE Run the basic pipeline with FastA reference with `fna` extension
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-fna_ref" -profile test_fna,docker --pairedEnd
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-fna_ref" -profile test_fna,docker --paired_end
       - name: REFERENCE Test with zipped reference input
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-gz_ref" -profile test,docker --pairedEnd --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-gz_ref" -profile test,docker --paired_end --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
       - name: FASTP Test fastp complexity filtering
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-fastp" -profile test,docker --pairedEnd --complexity_filter
-      - name: ADAPTERREMOVAL Test skip pairedEnd collapsing
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-fastp" -profile test,docker --paired_end --complexity_filter
+      - name: ADAPTERREMOVAL Test skip paired end collapsing
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skip_collapse" -profile test,docker --pairedEnd --skip_collapse
-      - name: ADAPTERREMOVAL Test pairedEnd collapsing but no trimming
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skip_collapse" -profile test,docker --paired_end --skip_collapse
+      - name: ADAPTERREMOVAL Test paired end collapsing but no trimming
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pretrim" -profile test_pretrim,docker --pairedEnd --skip_trim
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pretrim" -profile test_pretrim,docker --paired_end --skip_trim
       - name: ADAPTERREMOVAL Run the basic pipeline with paired end data without adapterRemoval
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skip_adapterremoval" -profile test,docker --pairedEnd --skip_adapterremoval
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skip_adapterremoval" -profile test,docker --paired_end --skip_adapterremoval
       - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end option
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-preserve5p" -profile test,docker --pairedEnd --preserve5p
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-preserve5p" -profile test,docker --paired_end --preserve5p
       - name: ADAPTERREMOVAL Run the basic pipeline with merged only option
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mergedonly" -profile test,docker --pairedEnd --mergedonly
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mergedonly" -profile test,docker --paired_end --mergedonly
       - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end and merged reads only options
         run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-preserve5p_mergedonly" -profile test,docker --pairedEnd --preserve5p --mergedonly
+         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-preserve5p_mergedonly" -profile test,docker --paired_end --preserve5p --mergedonly
       - name: MAPPER_CIRCULARMAPPER Test running with CircularMapper
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-circularmapper" -profile test,docker --pairedEnd --mapper 'circularmapper' --circulartarget 'NC_007596.2'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-circularmapper" -profile test,docker --paired_end --mapper 'circularmapper' --circulartarget 'NC_007596.2'
       - name: MAPPER_BWAMEM Test running with BWA Mem
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-bwa_mem" -profile test,docker --pairedEnd --mapper 'bwamem'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-bwa_mem" -profile test,docker --paired_end --mapper 'bwamem'
       - name: STRIP_FASTQ Run the basic pipeline with output unmapped reads as fastq
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-stripfastq" -profile test,docker --pairedEnd --strip_input_fastq
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-stripfastq" -profile test,docker --paired_end --strip_input_fastq
       - name: BAM_FILTERING Run basic mapping pipeline with mapping quality filtering, and unmapped export
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-unmapped_export" -profile test,docker --pairedEnd --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_umapped --bam_unmapped_type 'fastq'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-unmapped_export" -profile test,docker --paired_end --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_umapped --bam_unmapped_type 'fastq'
       - name: GENOTYPING_HC Test running GATK HaplotypeCaller
         run: |
-         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-haplotypercaller" -profile test_fna,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
+         nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-haplotypercaller" -profile test_fna,docker --paired_end  --dedupper 'dedup' --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
       - name: GENOTYPING_FB Test running FreeBayes
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-freebayes" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-freebayes" -profile test,docker --paired_end  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes'
       - 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'
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --single_end --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
+      #    nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-pmd_trimbam_gatkUG_MVA" -profile test,docker --paired_end  --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
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-MVA_additionalvcfs" -profile test,docker --paired_end  --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
+      #   nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-vcf2genome" -profile test,docker --paired_end  --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 "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
@@ -108,20 +114,20 @@ jobs:
           for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P databases/malt/; done
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-malt" -profile test,docker --pairedEnd --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --database "/home/runner/work/eager/eager/databases/malt/"
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-malt" -profile test,docker --paired_end --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --database "/home/runner/work/eager/eager/databases/malt/"
       - name: MALTEXTRACT Download resource files
         run: |
             mkdir -p databases/maltextract
             for i in ncbi.tre ncbi.map; do wget https://github.com/rhuebler/HOPS/raw/0.33/Resources/"$i" -P databases/maltextract/; done
       - name: MALTEXTRACT Basic with MALT plus MaltExtract
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-maltextract" -profile test,docker --pairedEnd --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' 
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-maltextract" -profile test,docker --paired_end --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' 
       - name: SEXDETERMINATION Run the basic pipeline with the bam input profile, but don't convert BAM, skip everything but sex determination
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-sexdeterrmine" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_sexdeterrmine
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-sexdeterrmine" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --single_end --run_sexdeterrmine
       - name: NUCLEAR CONTAMINATION Run basic pipeline with bam input profile, but don't convert BAM, skip everything but nuclear contamination estimation
         run: |
-          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-nuclear_contamination" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_nuclear_contamination
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-nuclear_contamination" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --single_end --run_nuclear_contamination
       - 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
+          nextflow run ${GITHUB_WORKSPACE} "$TOWER" -name "$RUN_NAME-mtnucratio" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --single_end --skip_preseq --skip_damage_calculation --run_mtnucratio
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index eef48337b..000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,103 +0,0 @@
-sudo: required
-language: python
-jdk: openjdk8
-services: docker
-python: '3.6'
-cache: pip
-matrix:
-  fast_finish: true
-
-before_install:
-  # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
-  # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/eager:dev
-  # Fake the tag locally so that the pipeline runs properly
-  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/eager:dev nfcore/eager:dev
-
-install:
-  # Install Nextflow
-  - mkdir /tmp/nextflow && cd /tmp/nextflow
-  - wget -qO- get.nextflow.io | bash
-  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-  # Install nf-core/tools
-  - pip install --upgrade pip
-  - pip install nf-core
-  # Install Conda 
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  - bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  # Reset
-  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
-  # Install markdownlint-cli
-  - sudo apt-get install npm && npm install -g markdownlint-cli
-
-env:
-  - NXF_VER='19.10.0' NXF_ANSI_LOG=0 RUN_NAME="eager-${TRAVIS_PULL_REQUEST_BRANCH}-${TRAVIS_JOB_NUMBER}" # Specify a minimum NF version that should be tested and work
-
-script:
-  # Lint the pipeline code
-  - nf-core lint ${TRAVIS_BUILD_DIR}
-  # REFERENCE: Run the basic pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-basic" -profile test,docker --pairedEnd --saveReference
-  # REFERENCE: Run the basic pipeline with single end data (pretending its single end actually) and all prepared index files
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-singleEnd" -profile test,docker --singleEnd
-  # REFERENCE: Run the basic pipeline with FastA reference with `fna` extension
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-fna_ref" -profile test_fna,docker --pairedEnd --saveReference
-  # REFERENCE: Test using pre-computed indices from a separate run beforehand
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preindex_ref" -profile test_fna,docker --pairedEnd --bwa_index 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fna' --fasta_index 'results/reference_genome/fasta_index/Mammoth_MT_Krause.fna.fai' --seq_dict 'results/reference_genome/seq_dict/Mammoth_MT_Krause.dict'
-  # REFERENCE: Test with zipped reference input
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-gz_ref" -profile test,docker --pairedEnd --fasta 'https://github.com/jfy133/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
-  # FASTP: Run the same pipeline testing optional steps of fastp, complexity 
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-fastp" -profile test,docker --pairedEnd --complexity_filter
-  # ADAPTERREMOVAL: Run the basic pipeline with paired end data without collapsing
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skip_collapse" -profile test,docker --pairedEnd --skip_collapse
-  # ADAPTERREMOVAL: Run the basic pipeline with paired end data without trimming, but still merge
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pretrim" -profile test_pretrim,docker --pairedEnd --skip_trim
-  # ADAPTERREMOVAL: Run the basic pipeline with paired end data without adapterRemoval
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skip_adapterremoval" -profile test,docker --pairedEnd --skip_adapterremoval
-  # ADAPTERREMOVAL: Run the basic pipeline with preserve5p end option
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preserve5p" -profile test,docker --pairedEnd --preserve5p
-  # ADAPTERREMOVAL: Run the basic pipeline with merged only option
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-mergedonly" -profile test,docker --pairedEnd --mergedonly
-  # ADAPTERREMOVAL: Run the basic pipeline with preserve5p end and merged reads only options
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preserve5p_mergedonly" -profile test,docker --pairedEnd --preserve5p --mergedonly
-  # MAPPER_CIRCULARMAPPER: Test running with CircularMapper
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-circularmapper" -profile test,docker --pairedEnd --mapper 'circularmapper' --circulartarget 'NC_007596.2'
-  # MAPPER_BWAMEM: Test running with BWA Mem
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-bwa_mem" -profile test,docker --pairedEnd --mapper 'bwamem'
-  # STRIP_FASTQ: Run the basic pipeline with output unmapped reads as fastq
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-stripfastq" -profile test,docker --pairedEnd --strip_input_fastq
-  # BAM_FILTERING: Run basic mapping pipeline with mapping quality filtering, and unmapped export
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-unmapped_export" -profile test,docker --pairedEnd --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_umapped --bam_unmapped_type 'fastq'
-  # GENOTYPING_HC: Test running GATK HaplotypeCaller
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-haplotypercaller" -profile test_fna,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
-  # GENOTYPING_FB: Test running FreeBayes
-  - 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
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_convertbam_basic" -profile test_bam,docker --bam --run_convertbam
-  # METAGENOMIC Download database and Run the basic pipeline but with unmapped reads going into MALT
-  - mkdir -p ${TRAVIS_BUILD_DIR}/databases/malt && for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P "${TRAVIS_BUILD_DIR}/databases/malt/"; done
-  - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-malt" -profile test,docker --pairedEnd --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --database "${TRAVIS_BUILD_DIR}/databases/malt/"
-  # MALTEXTRACT Download NCBI db, ncbi map/tree, additional files and run test
-  - mkdir -p ${TRAVIS_BUILD_DIR}/databases/maltextract && for i in ncbi.tre ncbi.map; do wget https://github.com/rhuebler/HOPS/raw/external/Resources/"$i" -P ${TRAVIS_BUILD_DIR}/databases/maltextract/; done
-  - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-maltextract" -profile test,docker --pairedEnd --run_bam_filtering --bam_discard_unmapped --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "${TRAVIS_BUILD_DIR}/databases/malt/" --run_maltextract --maltextract_ncbifiles "${TRAVIS_BUILD_DIR}/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' 
-  # SEXDETERMINAION: Run the basic pipeline with the bam input profile, but don't convert BAM, skip everything but sex determination
-  - nextflow run ${TRAVIS_BUILD_DIR} "$TOWER" -name "$RUN_NAME-sexdeterrmine" -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --skip_preseq --skip_damage_calculation --run_sexdeterrmine
-  # NUCLEAR CONTAMINATION ESTIMATION Premapped BAM run skipping most steps but run nuclear contamination with ANGSD
-  - 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
-
-
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1296d6b69..ba6816e8d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,7 +24,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Fancy new logo from [ZandraFagernas](https://github.com/ZandraFagernas)
 * [#286](https://github.com/nf-core/eager/issues/286) - Adds pipeline-specific profiles (loaded from nf-core configs)
 * [#310](https://github.com/nf-core/eager/issues/310) - Generalises base.config
-* [#326](https://github.com/nf-core/eager/pull/326) - Add Biopython and [xopen](https://github.com/marcelm/xopen/) dependancies  
+* [#326](https://github.com/nf-core/eager/pull/326) - Add Biopython and [xopen](https://github.com/marcelm/xopen/) dependencies  
 
 ### `Fixed`
 
@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#237](https://github.com/nf-core/eager/issues/237) - Fixed and Updated script scrape_software_versions
 * [#322](https://github.com/nf-core/eager/pull/322) - Move extract map reads fastq compression to pigz
 * [#327](https://github.com/nf-core/eager/pull/327) - Speed up strip_input_fastq process and make it more robust
+* [#342](https://github.com/nf-core/eager/pull/342) - Updated to match nf-core tools 1.8 linting guidelines
 
 ### `Dependencies`
 
diff --git a/Dockerfile b/Dockerfile
index 7bd109a7d..93eaa979e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,7 @@
-FROM nfcore/base:1.7
+FROM nfcore/base:1.8
 
 LABEL description="Docker image containing all requirements for nf-core/eager pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
+RUN conda env export --name nf-core-eager-2.1.0dev > nf-core-eager-2.1.0dev.yml
 ENV PATH /opt/conda/envs/nf-core-eager-2.1.0dev/bin:$PATH
diff --git a/README.md b/README.md
index 3e0d73766..75a30d80b 100644
--- a/README.md
+++ b/README.md
@@ -81,7 +81,7 @@ Additional functionality contained by the pipeline currently includes:
 
 4. Test the pipeline using the provided test data
 
-        nextflow run nf-core/eager -profile <docker/singularity/conda>,test --pairedEnd
+        nextflow run nf-core/eager -profile <docker/singularity/conda>,test --paired_end
 
 5. Start running your own ancient DNA analysis!
 
diff --git a/conf/test.config b/conf/test.config
index 244083be0..88c0a2d6b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -16,7 +16,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  singleEnd = false
+  single_end = false
   readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ['JK2802_AGAATAACCTACCA_L008', ['https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2802_AGAATAACCTACCA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ]
diff --git a/conf/test_bam.config b/conf/test_bam.config
index deb7bf8a8..1a2925ba9 100644
--- a/conf/test_bam.config
+++ b/conf/test_bam.config
@@ -16,7 +16,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  singleEnd = true
+  single_end = true
   readPaths = 'https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/bam/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped.bam'
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
diff --git a/conf/test_fna.config b/conf/test_fna.config
index 5519df04c..aa661c4a9 100644
--- a/conf/test_fna.config
+++ b/conf/test_fna.config
@@ -16,7 +16,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  singleEnd = false
+  single_end = false
   readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ['JK2802_AGAATAACCTACCA_L008', ['https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2802_AGAATAACCTACCA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ]
diff --git a/conf/test_humanbam.config b/conf/test_humanbam.config
index e9b3059a4..c65be53d6 100644
--- a/conf/test_humanbam.config
+++ b/conf/test_humanbam.config
@@ -16,7 +16,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  singleEnd = true
+  single_end = true
   reads = 'https://github.com/nf-core/test-datasets/raw/eager/testdata/Human/bam/JK2067_downsampled_s0.1.bam'
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
diff --git a/conf/test_pretrim.config b/conf/test_pretrim.config
index 68de624ff..3632e63ea 100644
--- a/conf/test_pretrim.config
+++ b/conf/test_pretrim.config
@@ -16,7 +16,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  singleEnd = false
+  single_end = false
   readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.pair1.truncated.fq.gz','https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/fastq/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.pair2.truncated.fq.gz']],
   ]
   // Genome references
diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
index d390c07f7..01a73a255 100644
--- a/docs/troubleshooting.md
+++ b/docs/troubleshooting.md
@@ -25,7 +25,7 @@ If no file, only one input file, or only read one and not read two is picked up
 1. The path must be enclosed in quotes (`'` or `"`)
 2. The path must have at least one `*` wildcard character. This is even if you are only running one paired end sample.
 3. When using the pipeline with paired end data, the path must use `{1,2}` or `{R1,R2}` notation to specify read pairs.
-4. If you are running Single end data make sure to specify `--singleEnd`
+4. If you are running Single end data make sure to specify `--single_end`
 
 If the pipeline can't find your files then you will get the following error
 
diff --git a/docs/usage.md b/docs/usage.md
index 389d54133..18629480c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -184,37 +184,37 @@ If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
 
 **Note**: It is not possible to run a mixture of single-end and paired-end files in one run.
 
-#### `--singleEnd`
+#### `--single_end`
 
-If you have single-end data or BAM files, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+If you have single-end data or BAM files, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
 
 ```bash
---singleEnd --reads 'path/to/data/*.fastq'
+--single_end --reads 'path/to/data/*.fastq'
 ```
 
 for a single sample, or
 
 ```bash
---singleEnd --reads 'path/to/data/*/*.fastq'
+--single_end --reads 'path/to/data/*/*.fastq'
 ```
 
 for multiple samples, where each sample's FASTQs are in it's own directory (indicated by the first `*`)
 
 **Note**: It is not possible to run a mixture of single-end and paired-end files in one run.
 
-#### `--pairedEnd`
+#### `--paired_end`
 
-If you have paired-end data, you need to specify `--pairedEnd` on the command line when you launc hthe pipeline.
+If you have paired-end data, you need to specify `--paired_end` on the command line when you launc hthe pipeline.
 
 A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
 
 ```bash
---pairedEnd --reads '*.fastq'
+--paired_end --reads '*.fastq'
 ```
 
 #### `--bam`
 
-Specifies the input file type to `--reads` is in BAM format. This is only valid in combination with `--singleEnd`.
+Specifies the input file type to `--reads` is in BAM format. This is only valid in combination with `--single_end`.
 
 #### `--fasta`
 
@@ -299,7 +299,7 @@ For example:
 ```bash
 nextflow run nf-core/eager \
 -profile test,docker \
---pairedEnd \
+--paired_end \
 --reads '*{R1,R2}*.fq.gz'
 --fasta 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta' \
 --bwa_index 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta'
@@ -491,7 +491,7 @@ Turns off the paired-end read merging.
 For example
 
 ```bash
---pairedEnd --skip_collapse  --reads '*.fastq'
+--paired_end --skip_collapse  --reads '*.fastq'
 ```
 
 #### `--skip_trim`
@@ -501,7 +501,7 @@ Turns off adaptor and quality trimming.
 For example:
 
 ```bash
---pairedEnd --skip_trim  --reads '*.fastq'
+--paired_end --skip_trim  --reads '*.fastq'
 ```
 
 #### `--preserve5p`
diff --git a/main.nf b/main.nf
index 4adbd312e..4adc494fc 100644
--- a/main.nf
+++ b/main.nf
@@ -29,8 +29,8 @@ def helpMessage() {
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes). For paired end data, the path must use '{1,2}' notation to specify read pairs
       -profile                      Institution or personal hardware config to use (e.g. standard, docker, singularity, conda, aws). Ask your system admin if unsure, or check documentation
-      --singleEnd                   Specifies that the input is single end reads (required if not pairedEnd)
-      --pairedEnd                   Specifies that the input is paired end reads (required if not singleEnd)
+      --single_end                   Specifies that the input is single end reads (required if not paired_end)
+      --paired_end                   Specifies that the input is paired end reads (required if not single_end)
       --bam                         Specifies that the input is in BAM format
       --fasta                       Path and name of FASTA reference file (required if not iGenome reference). File suffixes can be: '.fa', '.fn', '.fna', '.fasta'
       --genome                      Name of iGenomes reference (required if not fasta reference)
@@ -297,8 +297,8 @@ if (params.bam && !params.run_convertbam && !params.skip_adapterremoval ) {
 }
 
 // Validate BAM is single end only
-if (params.bam && !params.singleEnd){
-    exit 1, "BAM input must be used with --singleEnd "
+if (params.bam && !params.single_end){
+    exit 1, "BAM input must be used with --single_end "
 }
 
 // Validate that you're not trying to pass FASTQs to BAM only processes
@@ -311,15 +311,15 @@ if (params.bam && !params.run_convertbam && !params.skip_mapping) {
   exit 1, "You can't directly map a BAM file! Please supply the --run_convertbam parameter!"
 }
 
-// Validate that either pairedEnd or singleEnd has been specified by the user!
-if( params.singleEnd || params.pairedEnd || params.bam){
+// Validate that either paired_end or single_end has been specified by the user!
+if( params.single_end || params.paired_end || params.bam){
 } else {
-    exit 1, "Please specify either --singleEnd, --pairedEnd to execute the pipeline on FastQ files and --bam for previously processed BAM files!"
+    exit 1, "Please specify either --single_end, --paired_end to execute the pipeline on FastQ files and --bam for previously processed BAM files!"
 }
 
-// Validate that skip_collapse is only set to True for pairedEnd reads!
-if (params.skip_collapse  && params.singleEnd){
-    exit 1, "--skip_collapse can only be set for pairedEnd samples!"
+// Validate that skip_collapse is only set to True for paired_end reads!
+if (params.skip_collapse  && params.single_end){
+    exit 1, "--skip_collapse can only be set for paired_end samples!"
 }
 
 // Strip mode sanity checking
@@ -502,7 +502,7 @@ if( workflow.profile == 'awsbatch') {
 // is NOT read paths && BAM
 
 if( params.readPaths ){
-    if( params.singleEnd && !params.bam) {
+    if( params.single_end && !params.bam) {
         Channel
             .from( params.readPaths )
             .filter { it =~/.*.fastq.gz|.*.fq.gz|.*.fastq|.*.fq/ }
@@ -532,10 +532,10 @@ if( params.readPaths ){
     }
 } else if (!params.bam){
      Channel
-        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
+        .fromFilePairs( params.reads, size: params.single_end ? 1 : 2 )
         .filter { it =~/.*.fastq.gz|.*.fq.gz|.*.fastq|.*.fq/ }
         .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs " +
-            "to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nValid input file types: .fastq.gz', '.fq.gz', '.fastq', or '.fq'\nIf this is single-end data, please specify --singleEnd on the command line." }
+            "to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nValid input file types: .fastq.gz', '.fq.gz', '.fastq', or '.fq'\nIf this is single-end data, please specify --single_end on the command line." }
         .into { ch_input_for_skipconvertbam; ch_input_for_convertbam; ch_input_for_indexbam  }
 
 } else {
@@ -560,7 +560,7 @@ summary['Reads']        = params.reads
 summary['Fasta Ref']    = params.fasta
 summary['BAM Index Type'] = (params.large_ref == "") ? 'BAI' : 'CSI'
 if(params.bwa_index) summary['BWA Index'] = params.bwa_index
-summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
+summary['Data Type']    = params.single_end ? 'Single-End' : 'Paired-End'
 summary['Skipping FASTQC?'] = params.skip_fastqc ? 'Yes' : 'No'
 summary['Skipping AdapterRemoval?'] = params.skip_adapterremoval ? 'Yes' : 'No'
 if (!params.skip_adapterremoval) {
@@ -876,7 +876,7 @@ process fastp {
     file("*.json") into ch_fastp_for_multiqc
 
     script:
-    if(params.singleEnd){
+    if(params.single_end){
     """
     fastp --in1 ${reads[0]} --out1 "${reads[0].baseName}.pG.fq.gz" -A -g --poly_g_min_len "${params.complexity_filter_poly_g_min}" -Q -L -w ${task.cpus} --json "${reads[0].baseName}"_fastp.json 
     """
@@ -927,7 +927,7 @@ process adapter_removal {
     mergedonly = params.mergedonly ? "Y" : "N"
     
     //PE mode, dependent on trim_me and collapse_me the respective procedure is run or not :-) 
-    if (!params.singleEnd && !params.skip_collapse && !params.skip_trim){
+    if (!params.single_end && !params.skip_collapse && !params.skip_trim){
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} ${trim_me} --gzip --threads ${task.cpus} ${collapse_me} ${preserve5p}
@@ -946,14 +946,14 @@ process adapter_removal {
     mv *.settings output/
     """
     //PE, don't collapse, but trim reads
-    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim) {
+    } else if (!params.single_end && params.skip_collapse && !params.skip_trim) {
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} ${trim_me} ${collapse_me} ${preserve5p}
     mv *.settings ${base}.pair*.truncated.gz output/
     """
     //PE, collapse, but don't trim reads
-    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim) {
+    } else if (!params.single_end && !params.skip_collapse && params.skip_trim) {
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} ${collapse_me} ${trim_me}
@@ -1039,7 +1039,7 @@ process bwa {
     fasta = "${index}/${bwa_base}"
 
     //PE data without merging, PE data without any AR applied
-    if (!params.singleEnd && (params.skip_collapse || params.skip_adapterremoval)){
+    if (!params.single_end && (params.skip_collapse || params.skip_adapterremoval)){
     prefix = "${reads[0].baseName}"
     """
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -1109,7 +1109,7 @@ process circularmapper{
     
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && params.skip_collapse ){
+    if (!params.single_end && params.skip_collapse ){
     prefix = "${reads[0].baseName}"
     """ 
     bwa aln -t ${task.cpus} $elongated_root ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -1153,7 +1153,7 @@ process bwamem {
     prefix = "${reads[0].baseName}"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && params.skip_collapse){
+    if (!params.single_end && params.skip_collapse){
     """
     bwa mem -t ${task.cpus} $fasta ${reads[0]} ${reads[1]} -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".mapped.bam
     samtools index "${size}" -@ ${task.cpus} "${prefix}".mapped.bam
@@ -1317,7 +1317,7 @@ process strip_input_fastq {
 
 
     script:
-    if (params.singleEnd) {
+    if (params.single_end) {
         out_fwd = bam.baseName+'.stripped.fq.gz'
         """
         samtools index $bam
@@ -1388,7 +1388,7 @@ process dedup{
     treat_merged="${params.dedup_all_merged}" ? '-m' : ''
     size = "${params.large_ref}" ? '-c' : ''
     
-    if(params.singleEnd) {
+    if(params.single_end) {
     """
     dedup -i $bam $treat_merged -o . -u 
     mv *.log dedup.log
diff --git a/nextflow.config b/nextflow.config
index 87c8635f1..cd0544708 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -8,8 +8,8 @@
 params {
   //Pipeline options
     //Input reads
-  singleEnd = false
-  pairedEnd = false
+  single_end = false
+  paired_end = false
   reads = "data/*{1,2}.fastq.gz"
   readPaths = false
   bam = false
@@ -204,7 +204,7 @@ params {
   tracedir = "${params.outdir}/pipeline_info"
   awsqueue = false
   awsregion = 'eu-west-1'
-  igenomesIgnore = false
+  igenomes_ignore = false
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false
@@ -252,7 +252,7 @@ profiles {
   test_pretrim { includeConfig 'conf/test_pretrim.config' }
 }
 // Load igenomes.config if required
-if(!params.igenomesIgnore){
+if(!params.igenomes_ignore){
   includeConfig 'conf/igenomes.config'
 }
 // Capture exit codes from upstream processes when piping