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Dsl1 2.5.0 #2434

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Dsl1 2.5.0

Dsl1 2.5.0 #2434

Workflow file for this run

.github/workflows/ci.yml at 83163bb
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
# Uncomment if we need an edge release of Nextflow again
# env: NXF_EDGE: 1
jobs:
test:
name: Run workflow tests
# Only run on push if this is the nf-core dev branch (merged PRs)
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/eager') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions: check pipeline minimum and current latest
nxf_ver: ["20.07.1", "22.10.6"]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Check if Dockerfile or Conda environment changed
uses: technote-space/get-diff-action@v4
with:
FILES: |
Dockerfile
environment.yml
- name: Build new docker image
if: env.MATCHED_FILES
run: docker build --no-cache . -t nfcore/eager:2.4.7
- name: Pull docker image
if: ${{ !env.MATCHED_FILES }}
run: |
docker pull nfcore/eager:dev
docker tag nfcore/eager:dev nfcore/eager:2.4.7
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: HELPTEXT Run with the help flag
run: |
nextflow run ${GITHUB_WORKSPACE} --help
- name: Get test data for cases where we don't use TSV input
run: |
git clone --single-branch --branch eager https://github.com/nf-core/test-datasets.git data
- name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
run: |
if [[ $NXF_VER = '' ]]; then sleep 1200; fi
- name: BASIC Run the basic pipeline with directly supplied single-end FASTQ
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end
- name: BASIC Run the basic pipeline with directly supplied paired-end FASTQ
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz'
- name: BASIC Run the basic pipeline with supplied --input BAM
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end
- name: BASIC Run the basic pipeline with the test profile with, PE/SE, bwa aln
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --save_reference
- name: REFERENCE Basic workflow, with supplied indices
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/' --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} -profile test_tsv_fna,docker
- name: REFERENCE Test with zipped reference input
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --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} -profile test,docker --complexity_filter_poly_g
- name: ADAPTERREMOVAL Test skip paired end collapsing
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_collapse
- name: ADAPTERREMOVAL Test paired end collapsing but no trimming
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_pretrim,docker --skip_trim
- name: ADAPTERREMOVAL Run the basic pipeline with paired end data without adapterRemoval
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_adapterremoval
- name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end option
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p
- name: ADAPTERREMOVAL Run the basic pipeline with merged only option
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mergedonly
- name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end and merged reads only options
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p --mergedonly
- name: ADAPTER LIST Run the basic pipeline using an adapter list
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt'
- name: ADAPTER LIST Run the basic pipeline using an adapter list, skipping adapter removal
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval
- name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming
- name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming, but skip adapterremoval
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming --skip_adapterremoval
- name: MAPPER_CIRCULARMAPPER Test running with CircularMapper
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
- name: MAPPER_BWAMEM Test running with BWA Mem
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem' --skip_collapse
- name: MAPPER_BT2 Test running with BowTie2
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
- name: HOST_REMOVAL_FASTQ Run the basic pipeline with output unmapped reads as fastq
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --hostremoval_input_fastq
- name: BAM_FILTERING Run basic mapping pipeline with mapping quality filtering, and unmapped export
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_unmapped_type 'fastq'
- name: BAM_FILTERING Run basic mapping pipeline with post-mapping length filtering
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50
- name: PRESEQ Run basic mapping pipeline with different preseq mode
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10
- name: DEDUPLICATION Test with dedup
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --dedupper 'dedup' --dedup_all_merged
- name: BEDTOOLS Test bedtools feature annotation
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
- name: MAPDAMAGE2 damage calculation
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --damage_calculation_tool 'mapdamage'
- name: GENOTYPING_HC Test running GATK HaplotypeCaller
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
- name: GENOTYPING_FB Test running FreeBayes
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes'
- name: GENOTYPING_PC Test running pileupCaller
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'pileupcaller'
- name: GENOTYPING_ANGSD Test running ANGSD genotype likelihood calculation
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'angsd'
- name: GENOTYPING_BCFTOOLS Test running FreeBayes with bcftools stats turned on
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats
- name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
- name: TRIMBAM Test bamutils works alone
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_trim_bam
- name: PMDTOOLS Test PMDtools works alone
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_pmdtools
- name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_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 --genotyping_tool 'ug' --gatk_ug_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,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_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
- name: BAM_INPUT Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --run_convertinputbam
- name: METAGENOMIC Download MALT database
run: |
mkdir -p databases/malt
readlink -f databases/malt/
for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P databases/malt/; done
- name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output
- name: METAGENOMIC Run the basic pipeline but low-complexity filtered reads going into MALT
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter
- name: MALTEXTRACT Download resource files
run: |
mkdir -p databases/maltextract
for i in ncbi.tre ncbi.map; do wget https://github.com/rhuebler/HOPS/raw/0.33/Resources/"$i" -P databases/maltextract/; done
- name: MALTEXTRACT Basic with MALT plus MaltExtract
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --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: METAGENOMIC Run the basic pipeline but with unmapped reads going into Kraken
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_kraken,docker --run_bam_filtering --bam_unmapped_type 'fastq'
- name: SNPCAPTURE Run the basic pipeline with the bam input profile, generating statistics with a SNP capture bed
run: |
wget https://github.com/nf-core/test-datasets/raw/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz && gunzip 1240K.pos.list_hs37d5.0based.bed.gz
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --snpcapture_bed 1240K.pos.list_hs37d5.0based.bed
- 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} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --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} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --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} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio
- name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'