add nextflow d30e48d

nextflow/tests/checks/output-dsl.nf/.checks

@@ -0,0 +1,102 @@
+
+echo "Initial run"
+$NXF_RUN --save_bam_bai | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
+sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
+cmp .expected-text stdout.norm || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Run again with overwrite enabled and JSON output"
+$NXF_RUN -output-format json --save_bam_bai | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
+sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
+cmp .expected-json stdout.norm || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Run with some outputs disabled"
+rm -rf results
+
+$NXF_RUN -resume | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ ! -e results/align ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Resumed run"
+rm -rf results
+
+$NXF_RUN --save_bam_bai -resume | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false

nextflow/tests/checks/output-dsl.nf/.expected-json

@@ -0,0 +1,8 @@
+{
+    "samples": "/results/samples.csv",
+    "summary": {
+        "report": "/results/summary_report.html",
+        "data": "/results/summary_data/data.json",
+        "fastqc": "/results/summary_data/fastqc.txt"
+    }
+}

nextflow/tests/checks/output-dsl.nf/.expected-text

@@ -0,0 +1,11 @@
+
+Outputs:
+
+  /results
+
+  samples: samples.csv
+
+  summary:
+    report: summary_report.html
+    data: summary_data/data.json
+    fastqc: summary_data/fastqc.txt