diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl index db5ae2a..45970a9 100644 --- a/ReadbasedAnalysis.wdl +++ b/ReadbasedAnalysis.wdl @@ -163,7 +163,7 @@ task finish_reads { ln ${kraken2_report_tsv} ${prefix}_kraken2_report.tsv ln ${kraken2_krona_html} ${prefix}_kraken2_krona.html - /scripts/generate_object_json.py \ + /scripts/generate_object_json.py \ --type "nmdc:ReadBasedAnalysisActivity" \ --set read_based_taxonomy_analysis_activity_set \ --part ${proj} \ @@ -171,8 +171,8 @@ task finish_reads { was_informed_by=${informed_by} \ started_at_time=${start} \ ended_at_time=$end \ - execution_resource=${resource} \ - git_url=${git_url} \ + execution_resource="${resource}" \ + git_url=${git_url} \ version="v1.0.2-beta" \ --url ${url_root}${proj}/ReadbasedAnalysis/ \ --inputs ${input_file} \ diff --git a/ReadbasedAnalysisTasks.wdl b/ReadbasedAnalysisTasks.wdl index 230c391..9cb8be2 100644 --- a/ReadbasedAnalysisTasks.wdl +++ b/ReadbasedAnalysisTasks.wdl @@ -28,7 +28,7 @@ task profilerGottcha2 { cpu: CPU node: 1 nwpn: 1 - mem: "45G" + memory: "45G" time: "04:00:00" } meta { @@ -65,7 +65,7 @@ task profilerCentrifuge { cpu: CPU node: 1 nwpn: 1 - mem: "45G" + memory: "45G" time: "04:00:00" } meta { @@ -104,7 +104,7 @@ task profilerKraken2 { cpu: CPU node: 1 nwpn: 1 - mem: "45G" + memory: "45G" time: "04:00:00" } meta { @@ -128,7 +128,7 @@ task generateSummaryJson { docker: DOCKER node: 1 nwpn: 1 - mem: "45G" + memory: "45G" time: "04:00:00" } meta { @@ -164,4 +164,4 @@ task stage { maxRetries: 1 docker: container } -} \ No newline at end of file +} diff --git a/ReadbasedAnalysis_inputs.json b/ReadbasedAnalysis_inputs.json index 769c230..d4415c6 100644 --- a/ReadbasedAnalysis_inputs.json +++ b/ReadbasedAnalysis_inputs.json @@ -9,12 +9,11 @@ "kraken2": "/global/cfs/projectdirs/m3408/aim2/database/kraken2/", "centrifuge": "/global/cfs/projectdirs/m3408/aim2/database/centrifuge/p_compressed" }, - "ReadbasedAnalysis.reads": [ - "/path/to/SRR7877884.1.fastq.gz", - "/path/to/SRR7877884.2.fastq.gz" - ], + "ReadbasedAnalysis.input_file": "/path/to/test.fastq.gz", "ReadbasedAnalysis.paired": true, - "ReadbasedAnalysis.prefix": "SRR7877884", - "ReadbasedAnalysis.outdir": "/global/cfs/projectdirs/m3408/aim2/metagenome/ReadbasedAnalysis/SRR7877884", - "ReadbasedAnalysis.cpu": 8 + "ReadbasedAnalysis.prefix": "TEST", + "ReadbasedAnalysis.cpu": 8, + "ReadbasedAnalysis.proj": "TEST", + "ReadbasedAnalysis.resource": "NERSC - CORI", + "ReadbasedAnalysis.informed_by": "None" }