BUG+TST Data in a subdirectory cannot be collected

This tests #141. From the original report: > Parallel module exits with error, if the data are not in the same > directory as the script. Running the parallel.ngl test exits with > error, if data is moved into a subfolder.
ngless-toolkit · Dec 4, 2020 · f1296c0 · f1296c0
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diff --git a/tests/parallel_collect_subdir/cleanup.sh b/tests/parallel_collect_subdir/cleanup.sh
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+../parallel/cleanup.sh
diff --git a/tests/parallel_collect_subdir/count_many.ngl b/tests/parallel_collect_subdir/count_many.ngl
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+ngless "1.1"
+import "parallel" version "0.6"
+
+samples = readlines("samplefile")
+sample = lock1(samples)
+input = samfile(sample + ".sam.gz")
+
+counts = count(input, features=["exon", "gene", "start_codon", "stop_codon"], subfeatures=["gene_id"], multiple={1overN}, gff_file="short.gtf")
+collect(counts, ofile="output.RNA.txt", current=sample, allneeded=samples)
diff --git a/tests/parallel_collect_subdir/samplefile b/tests/parallel_collect_subdir/samplefile
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+subdir/sample1
diff --git a/tests/parallel_collect_subdir/short.gtf b/tests/parallel_collect_subdir/short.gtf
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+../../test_samples/short.gtf
diff --git a/tests/parallel_collect_subdir/subdir/sample.sam.gz b/tests/parallel_collect_subdir/subdir/sample.sam.gz
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+../../../test_samples/sample.sam.gz
diff --git a/tests/parallel_collect_subdir/subdir/sample1.sam.gz b/tests/parallel_collect_subdir/subdir/sample1.sam.gz
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+sample.sam.gz