Update e2e test

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
nextflow-io · Dec 12, 2024 · aa50499 · aa50499
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commit aa50499
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diff --git a/tests/checks/output-dsl.nf/.checks b/tests/checks/output-dsl.nf/.checks
@@ -0,0 +1,75 @@
+#
+# run normal mode
+#
+echo First run
+$NXF_RUN --save_bam_bai | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > fastqc'` == 3 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > quant'` == 3 ]] || false
+
+[[ -f results/fastqc/alpha.fastqc.log ]] || false
+[[ -f results/fastqc/beta.fastqc.log ]] || false
+[[ -f results/fastqc/delta.fastqc.log ]] || false
+[[ -f results/align/alpha.bai ]] || false
+[[ -f results/align/alpha.bam ]] || false
+[[ -f results/align/beta.bai ]] || false
+[[ -f results/align/beta.bam ]] || false
+[[ -f results/align/delta.bai ]] || false
+[[ -f results/align/delta.bam ]] || false
+[[ -L results/quant/alpha ]] || false
+[[ -L results/quant/beta ]] || false
+[[ -L results/quant/delta ]] || false
+[[ -f results/samples.csv ]] || false
+
+
+#
+# one more time to make sure 'overwrite' is fine
+#
+echo Second run
+$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
+
+[[ -f results/fastqc/alpha.fastqc.log ]] || false
+[[ -f results/fastqc/beta.fastqc.log ]] || false
+[[ -f results/fastqc/delta.fastqc.log ]] || false
+[[ -f results/align/alpha.bai ]] || false
+[[ -f results/align/alpha.bam ]] || false
+[[ -f results/align/beta.bai ]] || false
+[[ -f results/align/beta.bam ]] || false
+[[ -f results/align/delta.bai ]] || false
+[[ -f results/align/delta.bam ]] || false
+[[ -L results/quant/alpha ]] || false
+[[ -L results/quant/beta ]] || false
+[[ -L results/quant/delta ]] || false
+[[ -f results/samples.csv ]] || false
+
+
+#
+# clean & run resume mode
+#
+echo Third run
+rm -rf results
+
+$NXF_RUN --save_bam_bai -resume | 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
+
+[[ -f results/fastqc/alpha.fastqc.log ]] || false
+[[ -f results/fastqc/beta.fastqc.log ]] || false
+[[ -f results/fastqc/delta.fastqc.log ]] || false
+[[ -f results/align/alpha.bai ]] || false
+[[ -f results/align/alpha.bam ]] || false
+[[ -f results/align/beta.bai ]] || false
+[[ -f results/align/beta.bam ]] || false
+[[ -f results/align/delta.bai ]] || false
+[[ -f results/align/delta.bam ]] || false
+[[ -L results/quant/alpha ]] || false
+[[ -L results/quant/beta ]] || false
+[[ -L results/quant/delta ]] || false
+[[ -f results/samples.csv ]] || false
diff --git a/tests/output-dsl.nf b/tests/output-dsl.nf
@@ -64,7 +64,7 @@ process quant {
 
 workflow {
   main:
-  ids = Channel.of('1', '2', '3')
+  ids = Channel.of('alpha', 'beta', 'delta')
   ch_fastqc = fastqc(ids)
   (ch_bam, ch_bai) = align(ids)
   ch_quant = quant(ids)