Update 20240906 #28
Workflow file for this run
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| name: Test Grandeur workflow with additional fastani references | |
| on: [pull_request, workflow_dispatch] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| nextflow -version | |
| - name: Download fastas | |
| run: | | |
| mkdir fastas | |
| for accession in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1 | |
| do | |
| all=$(echo $accession | cut -f 2 -d "_") | |
| fir=$(echo $all | cut -c 1-3) | |
| mid=$(echo $all | cut -c 4-6) | |
| end=$(echo $all | cut -c 7-9) | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz | |
| gzip -d ${accession}_genomic.fna.gz | |
| mv ${accession}_genomic.fna fastas/. | |
| done | |
| - name: Download fastani refs for list | |
| run: | | |
| mkdir refs | |
| for accession in GCA_000240185.2_ASM24018v2 GCA_003812925.1_ASM381292v1 GCA_901421005.1_39282_A01 | |
| do | |
| all=$(echo $accession | cut -f 2 -d "_") | |
| fir=$(echo $all | cut -c 1-3) | |
| mid=$(echo $all | cut -c 4-6) | |
| end=$(echo $all | cut -c 7-9) | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz | |
| mv ${accession}_genomic.fna.gz refs/. | |
| done | |
| ls refs/* > fastani_ref_list.txt | |
| - name: Download fastani refs | |
| run: | | |
| for accession in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1 | |
| do | |
| all=$(echo $accession | cut -f 2 -d "_") | |
| fir=$(echo $all | cut -c 1-3) | |
| mid=$(echo $all | cut -c 4-6) | |
| end=$(echo $all | cut -c 7-9) | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz | |
| done | |
| ls refs/* > fastani_ref_list.txt | |
| - name: Run Grandeur with ref list | |
| run: | | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --fastani_ref_list fastani_ref_list.txt | |
| cat grandeur/grandeur_summary.tsv | |
| cat grandeur/summary/software_versions.yml | |
| ls grandeur/multiqc/multiqc_report.html | |
| - name: Run Grandeur with refs | |
| run: | | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas -resume --fastani_ref GCA_009665515.2_ASM966551v2_genomic.fna.gz,GCA_009763645.1_ASM976364v1_genomic.fna.gz --outdir grandeur2 | |
| cat grandeur2/grandeur_summary.tsv | |
| cat grandeur2/summary/software_versions.yml | |
| ls grandeur2/multiqc/multiqc_report.html | |
| - name: Run Grandeur with refs and ref list | |
| run: | | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas -resume --fastani_ref_list fastani_ref_list.txt --fastani_ref GCA_009665515.2_ASM966551v2_genomic.fna.gz,GCA_009763645.1_ASM976364v1_genomic.fna.gz --outdir grandeur3 | |
| cat grandeur3/grandeur_summary.tsv | |
| cat grandeur3/summary/software_versions.yml | |
| ls grandeur3/multiqc/multiqc_report.html | |