Merge pull request #1047 from maxplanck-ie/KS

fix 1023
maxplanck-ie · Sep 5, 2024 · bfc7cb1 · bfc7cb1
2 parents 940287a + 598a87a
commit bfc7cb1
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -189,9 +189,9 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1157 ]; then exit 1 ; fi
 WC=`DNAmapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l `
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1249 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l `
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1388 ]; then exit 1 ; fi
 WC=`DNAmapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --aligner bwa-mem2 | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l `
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1296 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1388 ]; then exit 1 ; fi
 #allelic
 WC=`DNAmapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v -f .ci_stuff/test_ignore_patterns.txt | sed '/^\s*$/d' | sed '/^host:/d' | wc -l `
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 2237 ]; then exit 1 ; fi

diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile
@@ -73,7 +73,7 @@ if UMIDedup:
             {params.umitools_paired} {params.umitools_options}
             """
 else:
-    if aligner == "Bowtie2":
+    if aligner == "Bowtie2" or aligner == "bwa" or aligner == "bwa-mem2":
         rule filter_reads:
             input:
                 bamfile = "filtered_bam/{sample}.filtered.tmp.bam"
@@ -83,10 +83,10 @@ else:
                    mv {input.bamfile} {output.bamfile}
                    """
 
-    elif not (aligner=="bwameth" or aligner=="bwameth2") :
+    elif aligner == "STAR" or aligner == "HISAT2" :
         rule filter_reads:
             input:
-                bamfile = aligner+"/{sample}.bam"
+                bamfile = aligner + "/{sample}.bam"
             output:
                 bamfile = "filtered_bam/{sample}.filtered.bam"
             shell: """

diff --git a/tests/test_jobcounts.py b/tests/test_jobcounts.py
@@ -474,7 +474,7 @@ def test_bwa(self, ifs):
         print(' '.join([str(i) for i in ci]))
         _p = sp.run(ci, capture_output=True, text=True)
         assert _p.returncode == 0
-        assert parseSpOut(_p) == 143
+        assert parseSpOut(_p) == 152
     def test_bwa2(self, ifs):
         ci = [
             "DNAmapping",
@@ -493,7 +493,7 @@ def test_bwa2(self, ifs):
         print(' '.join([str(i) for i in ci]))
         _p = sp.run(ci, capture_output=True, text=True)
         assert _p.returncode == 0
-        assert parseSpOut(_p) == 143
+        assert parseSpOut(_p) == 152
     def test_se(self, ifs):
         ci = [
             "DNAmapping",