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Merge pull request #347 from UPHL-BioNGS/update-20240702
Update 20240702
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,134 @@ | ||
| params.vadr = false | ||
|
|
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| process { | ||
| withName:ivar_consensus{ | ||
| memory = '4 GB' | ||
| } | ||
| 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 }] | ||
| } | ||
| 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 }] | ||
| } | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| name: Test mpx workflow with yale primers | ||
|
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||
| on: [pull_request, workflow_dispatch] | ||
|
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| run-name: mpx_yale | ||
|
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| jobs: | ||
|
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| test: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@master | ||
|
|
||
| - name: Install Nextflow | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Download reads | ||
| run: | | ||
| mkdir reads | ||
| cd reads | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_1.fastq.gz | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_2.fastq.gz | ||
| cd ../ | ||
| - name: Run Cecret | ||
| run: | | ||
| nextflow run . -profile docker,mpx_yale -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 | ||
| ls cecret* | ||
| head cecret*/cecret_results.txt | ||
| - name: Clean | ||
| run: rm -rf work .nextflow* |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,8 @@ jobs: | |
| 'ncov_V3', | ||
| 'ncov_V4', | ||
| 'ncov_V4.1', | ||
| 'ncov_V5.3.2' | ||
| 'ncov_V5.3.2', | ||
| 'mpx_yale' | ||
| ] | ||
|
|
||
| steps: | ||
|
|
||
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