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Merged
jfy133 merged 1 commit into from
Sep 14, 2021
Merged

Test tsv to test #795

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68 changes: 34 additions & 34 deletions .github/workflows/ci.yml
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Expand Up @@ -62,91 +62,91 @@ jobs:
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,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end
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,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz'
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,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end
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_tsv,docker --save_reference
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --save_reference
- name: REFERENCE Basic workflow, with supplied indices
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,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'
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_tsv,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
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_tsv,docker --complexity_filter_poly_g
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_tsv,docker --skip_collapse
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_tsv,docker --skip_adapterremoval
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_tsv,docker --preserve5p
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_tsv,docker --mergedonly
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_tsv,docker --preserve5p --mergedonly
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_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt'
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_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval
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_tsv,docker --run_post_ar_trimming
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_tsv,docker --run_post_ar_trimming --skip_adapterremoval
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_tsv,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
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_tsv,docker --mapper 'bwamem'
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem'
- name: MAPPER_BT2 Test running with BowTie2
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
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_tsv,docker --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_unmapped_type 'fastq'
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_tsv,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50
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_tsv,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10
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_tsv,docker --dedupper 'dedup' --dedup_all_merged
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_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
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: 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_tsv,docker --run_genotyping --genotyping_tool 'freebayes'
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'
Expand All @@ -155,25 +155,25 @@ jobs:
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_tsv,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats
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_tsv,docker --run_trim_bam
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_trim_bam
- name: PMDTOOLS Test PMDtools works alone
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools
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_tsv,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
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_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
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 ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval
Expand All @@ -187,17 +187,17 @@ jobs:
for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P databases/malt/; done
- name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,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
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_tsv,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
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_tsv,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'
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'
Expand All @@ -212,4 +212,4 @@ jobs:
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_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
- [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them
- [#792](https://github.com/nf-core/eager/issues/792) Fixed java error messages for AdapterRemovalFixPrefix being hidden in output
- [#794](https://github.com/nf-core/eager/issues/794) Aligned default test profile with nf-core standards (`test_tsv` is now `test`)

### `Dependencies`

Expand Down
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -35,7 +35,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
3. Download the pipeline and test it on a minimal dataset with a single command:

```bash
nextflow run nf-core/eager -profile test_tsv,<docker/singularity/podman/shifter/charliecloud/conda/institute>
nextflow run nf-core/eager -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
```

> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
Expand Down
7 changes: 2 additions & 5 deletions conf/test.config
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Expand Up @@ -4,12 +4,11 @@
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/eager -profile test,<docker/singularity>
* nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
*/

includeConfig 'test_resources.config'


params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
Expand All @@ -19,9 +18,7 @@ params {
max_time = 48.h
genome = false
//Input data
single_end = false
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_fastq.tsv'
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
// Ignore `--input` as otherwise the parameter validation will throw an error
schema_ignore_params = 'genomes,input_paths,input'
}
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