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Merge pull request #172 from UPHL-BioNGS/refactoring
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| name: Test Grandeur workflow with additional fastani references | ||
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| on: [pull_request, workflow_dispatch] | ||
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| jobs: | ||
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| test: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
|
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| - 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 | ||
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| - 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 | ||
| - 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 | ||
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| - 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 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| process { | ||
| maxRetries = 0 | ||
| maxErrors = '-1' | ||
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| withLabel:process_single { | ||
| cpus = { 1 } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 10.m * task.attempt } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 2.h * task.attempt } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| } | ||
| withLabel:process_high { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 16.h * task.attempt } | ||
| } | ||
| withLabel:process_long { | ||
| time = { 20.h * task.attempt } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { 12.GB * task.attempt } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| name: Test Grandeur workflow with Klebsiella | ||
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| on: [pull_request, workflow_dispatch] | ||
|
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||
| 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: Run Grandeur | ||
| run: | | ||
| docker --version | ||
| mkdir fastas | ||
| 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 | ||
| gzip -d ${accession}_genomic.fna.gz | ||
| mv ${accession}_genomic.fna fastas/. | ||
| done | ||
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas | ||
| cat grandeur/grandeur_summary.tsv | ||
| - name: Check Klebsiella file | ||
| run: | | ||
| for file in grandeur/kleborate/kleborate_results.tsv | ||
| do | ||
| head $file | ||
| wc -l $file | ||
| done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| name: Test Grandeur workflow with Mycobacterium | ||
|
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| on: [pull_request, workflow_dispatch] | ||
|
|
||
| jobs: | ||
|
|
||
| test: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Install Nextflow | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| nextflow -version | ||
| - name: Run Grandeur | ||
| run: | | ||
| docker --version | ||
| mkdir fastas | ||
| for accession in GCA_010729105.1_ASM1072910v1 GCA_000195955.2_ASM19595v2 | ||
| do | ||
| all=$(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 | ||
| nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas | ||
| cat grandeur/grandeur_summary.tsv | ||
| - name: Check Mycobacterium file | ||
| run: | | ||
| for file in grandeur/drprg/drprg_summary.tsv grandeur/mykrobe/mykrobe_summary.csv | ||
| do | ||
| head $file | ||
| wc -l $file | ||
| done |
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