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erinyoung
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,134 +1,8 @@ | ||
| process { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| withName:aci{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:artic{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:artic_read_filtering{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:bbnorm{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:bcftools_variants{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:bwa{ | ||
| publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] | ||
| } | ||
| withName:download{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:fasta_prep{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:summary{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:unzip{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:fastp{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:fastqc{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:freyja_variants{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:freyja_demix{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:freyja_aggregate{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:heatcluster{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:igv_reports{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:iqtree2{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| withName:ivar_consensus{ | ||
| memory = '4 GB' | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:ivar_variants{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:ivar_trim{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:kraken2{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:mafft{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:minimap2{ | ||
| publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] | ||
| } | ||
| withName:multiqc_combine{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:nextclade_dataset{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:nextclade{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:pango_collapse{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:pangolin{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:phytreeviz{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_stats{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_coverage{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_flagstat{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_depth{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_ampliconstats{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_plot_ampliconstats{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_sort{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_filter{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_ampliconclip{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:samtools_markdup{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:seqyclean{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:snpdists{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| } | ||
| withName:vadr{ | ||
| publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] | ||
| memory = '4 GB' | ||
| } | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| sample,fastq_1,fastq_2 | ||
| paired_test,reads/SRR13957123_1.fastq.gz,reads/SRR13957123_2.fastq.gz | ||
| single_test,reads/SRR25097869.fastq.gz,single | ||
| wastewater_test,reads/SRR31220305_1.fastq.gz,reads/SRR31220305_2.fastq.gz | ||
| fasta_test,fastas/SRR13957123DB.fa,fasta | ||
| nanopore_test,nanopore/SRR31458670_1.fastq.gz,ont |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| name: Test SARS-CoV-2 workflow | ||
|
|
||
| on: [pull_request, workflow_dispatch] | ||
|
|
||
| run-name: Download fastq and fasta and run | ||
|
|
||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@master | ||
| with: | ||
| lfs: true | ||
|
|
||
| - name: Checkout LFS objects | ||
| run: git lfs checkout | ||
|
|
||
| - name: Install Nextflow | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Run Cecret | ||
| run: | | ||
| docker --version | ||
| mkdir reads | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_1.fastq.gz | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/023/SRR13957123/SRR13957123_2.fastq.gz | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR250/069/SRR25097869/SRR25097869.fastq.gz | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/005/SRR31220305/SRR31220305_1.fastq.gz | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/005/SRR31220305/SRR31220305_2.fastq.gz | ||
| mv *fastq.gz reads/. | ||
| mkdir -p fastas | ||
| wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa | ||
| mv SRR13957123.consensus.fa fastas/SRR13957123DB.fa | ||
| mkdir nanopore | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR314/070/SRR31458670/SRR31458670_1.fastq.gz | ||
| mv SRR31458670_1.fastq.gz nanopore/SRR31458670_1.fastq.gz | ||
| nextflow run . -profile docker -c .github/workflows/github_actions.config --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --sample_sheet .github/workflows/sample_sheet.csv | ||
| ls cecret* | ||
| cat cecret*/cecret_results.txt | ||
| - name: Clean | ||
| run: rm -rf work .nextflow* |
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