diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e87df3c..0d81b75 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -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 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 256bc9e..a1e3cf5 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -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 diff --git a/assets/samplesheet_assembly.csv b/assets/samplesheet_assembly.csv index 35945f5..2b5d2ed 100644 --- a/assets/samplesheet_assembly.csv +++ b/assets/samplesheet_assembly.csv @@ -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 diff --git a/assets/samplesheet_genomes.csv b/assets/samplesheet_genomes.csv index 4db4f00..95a64f4 100644 --- a/assets/samplesheet_genomes.csv +++ b/assets/samplesheet_genomes.csv @@ -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