fix: keep order of samples within snakemake

zavolanlab · Feb 20, 2024 · ef48042 · ef48042
1 parent 2afde9d
commit ef48042
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -38,8 +38,8 @@ snakemake \
     --report="snakemake_report.html"
 
 # Check md5 sum of some output files
-find results/ -type f -name \*\.gz -exec gunzip '{}' \;
-find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
+find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \;
+find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
 md5sum --check "expected_output.md5"
 
 # Check whether STAR produces expected alignments
@@ -49,15 +49,15 @@ md5sum --check "expected_output.md5"
 echo "Verifying STAR output"
 result=$(bedtools intersect -F 1 -v -bed \
     -a ../input_files/synthetic.mate_1.bed \
-    -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \
+    -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \
     | wc -l)
 if [ $result != "0" ]; then
     echo "Alignments for mate 1 reads are not consistent with ground truth"
     exit 1
 fi
 result=$(bedtools intersect -F 1 -v -bed \
     -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
-    -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \
+    -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \
     | wc -l)
 if [ $result != "0" ]; then
     echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -67,8 +67,8 @@ fi
 # Check whether Salmon assigns reads to expected genes
 echo "Verifying Salmon output"
 diff \
-    <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
 diff \
-    <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+    <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
     <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -20,7 +20,7 @@ def get_sample(column_id, search_id=None, search_value=None):
 
 def get_all_samples(search_id=None, search_value=None):
     return list(
-        set(samples_table.index[samples_table[search_id] == search_value].values)
+        pd.unique(samples_table.index[samples_table[search_id] == search_value].values)
     )