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added env variables to AWS tests #94

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added env variables to AWS tests #94

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4 changes: 4 additions & 0 deletions .github/workflows/awsfulltest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,10 @@ on:
release:
types: [published]

env:
WEBIN_ACCOUNT: ${{ secrets.WEBIN_ACCOUNT }}
WEBIN_PASSWORD: ${{ secrets.WEBIN_PASSWORD }}

jobs:
run-platform:
name: Run AWS full tests
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5 changes: 5 additions & 0 deletions .github/workflows/awstest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,11 @@ name: nf-core AWS test

on:
workflow_dispatch:

env:
WEBIN_ACCOUNT: ${{ secrets.WEBIN_ACCOUNT }}
WEBIN_PASSWORD: ${{ secrets.WEBIN_PASSWORD }}

jobs:
run-platform:
name: Run AWS tests
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2 changes: 1 addition & 1 deletion assets/samplesheet_assembly.csv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
sample,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version
sample1,tests/data/contigs.fasta.gz,tests/data/fastq_1.fastq,tests/data/fastq_2.fastq,,ERR000001,SPAdes,3.15
sample2,tests/data/invalid_assembly.fasta.gz,,,45,ERR000002,Velvet,1.2.10
sample3,tests/data/contigs.fasta.gz,,,30,ERR000003,MEGAHIT,1.2.9
2 changes: 1 addition & 1 deletion assets/samplesheet_genomes.csv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
sample,fasta,accession,fastq_1,fastq_2,assembly_software,binning_software,binning_parameters,stats_generation_software,completeness,contamination,genome_coverage,metagenome,co-assembly,broad_environment,local_environment,environmental_medium,RNA_presence,NCBI_lineage
id,fasta,accession,fastq_1,fastq_2,assembly_software,binning_software,binning_parameters,stats_generation_software,completeness,contamination,genome_coverage,metagenome,co-assembly,broad_environment,local_environment,environmental_medium,RNA_presence,NCBI_lineage
lachnospira_eligens,https://github.com/nf-core/test-datasets/raw/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz,SRR24458089,,,spades_v3.15.5,mags_v1,default,CheckM2_v1.0.1,61.0,0.21,32.07,sediment metagenome,No,marine,cable bacteria,marine sediment,No,d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfobacterales;f__Desulfobulbaceae;g__Candidatus Electrothrix;s__
lachnospiraceae,https://github.com/nf-core/test-datasets/raw/seqsubmit/test_data/bins/bin_lachnospiraceae.fa.gz,SRR24458087,,,spades_v3.15.5,mags_v1,default,CheckM2_v1.0.1,92.81,1.09,66.04,sediment metagenome,No,marine,cable bacteria,marine sediment,No,d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfobacterales;f__Desulfobulbaceae;g__Candidatus Electrothrix;s__Candidatus Electrothrix marina
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