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drpatelhdrpatelh
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Merge pull request #1026 from maxulysse/profile_test_data_base
PROFILES: test -> test_cache + restore test
2 parents 5539967 + cfe179a commit 9472aaa

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‎.github/workflows/ci.yml‎

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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_salmon:
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name: Test STAR Salmon with workflow parameters
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- name: Run pipeline with STAR and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_rsem:
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name: Test STAR RSEM with workflow parameters
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- name: Run pipeline with RSEM STAR and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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hisat2:
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name: Test HISAT2 with workflow parameters
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- name: Run pipeline with HISAT2 and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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salmon:
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name: Test Salmon with workflow parameters
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- name: Run pipeline with Salmon and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

‎conf/test.config‎

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// Input data
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// params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
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input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
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input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
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// Genome references
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fasta = "${params.test_data_base}/reference/genome.fasta"
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gtf = "${params.test_data_base}/reference/genes.gtf.gz"
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gff = "${params.test_data_base}/reference/genes.gff.gz"
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transcript_fasta = "${params.test_data_base}/reference/transcriptome.fasta"
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additional_fasta = "${params.test_data_base}/reference/gfp.fa.gz"
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bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
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hisat2_index = "${params.test_data_base}/reference/hisat2.tar.gz"
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salmon_index = "${params.test_data_base}/reference/salmon.tar.gz"
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rsem_index = "${params.test_data_base}/reference/rsem.tar.gz"
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta"
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gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz"
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transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta"
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additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz"
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bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt"
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hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz"
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salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz"
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rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz"
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// Other parameters
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skip_bbsplit = false

‎conf/test_cache.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/rnaseq -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
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input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
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// Genome references
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fasta = "${params.test_data_base}/reference/genome.fasta"
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gtf = "${params.test_data_base}/reference/genes.gtf.gz"
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gff = "${params.test_data_base}/reference/genes.gff.gz"
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transcript_fasta = "${params.test_data_base}/reference/transcriptome.fasta"
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additional_fasta = "${params.test_data_base}/reference/gfp.fa.gz"
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bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
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hisat2_index = "${params.test_data_base}/reference/hisat2.tar.gz"
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salmon_index = "${params.test_data_base}/reference/salmon.tar.gz"
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rsem_index = "${params.test_data_base}/reference/rsem.tar.gz"
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// Other parameters
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skip_bbsplit = false
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pseudo_aligner = 'salmon'
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umitools_bc_pattern = 'NNNN'
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}
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// When using RSEM, remove warning from STAR whilst building tiny indices
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process {
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withName: 'RSEM_PREPAREREFERENCE_GENOME' {
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ext.args2 = "--genomeSAindexNbases 7"
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}
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}

‎nextflow.config‎

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public_aws_ecr {
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includeConfig 'conf/public_aws_ecr.config'
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}
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test { includeConfig 'conf/test.config' }
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test_cache { includeConfig 'conf/test_cache.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_full_aws {
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includeConfig 'conf/test_full.config'
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}

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