Merge pull request #163 from FrickTobias/variants

Changed VCF file naming
FrickTobias · Nov 29, 2019 · 338bbd6 · 338bbd6
2 parents 7f6cfc3 + ad9b0c6
commit 338bbd6
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Showing 3 changed files with 38 additions and 28 deletions.
diff --git a/src/blr/Snakefile b/src/blr/Snakefile
@@ -178,19 +178,19 @@ rule bam_to_fastq:
         " -2 {output.r2_fastq} 2>> {log}"
 
 
-if config["reference_variants"]:
-    rule link:
-        output: "reference.vcf"
-        shell:
-            "ln -s {config[reference_variants]} {output}"
-else:
-    rule call_variants_freebayes:
-        output:
-             vcf = "reference.vcf"
-        input:
-             bam = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.bam"
-        log: "call_variants_freebayes.log"
-        shell:
-             "freebayes"
-             " -f {config[genome_reference]}"
-             " {input.bam} 1> {output.vcf} 2> {log}"
+rule symlink_reference_variants:
+    output: "variants.reference.vcf"
+    shell:
+        "ln -s {config[reference_variants]} {output}"
+
+
+rule call_variants_freebayes:
+    output:
+         vcf = "variants.called.vcf"
+    input:
+         bam = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.bam"
+    log: "call_variants_freebayes.log"
+    shell:
+         "freebayes"
+         " -f {config[genome_reference]}"
+         " {input.bam} 1> {output.vcf} 2> {log}"
diff --git a/src/blr/rules/phasing.smk b/src/blr/rules/phasing.smk
@@ -1,10 +1,12 @@
 
+variants = "variants.reference.vcf" if config["reference_variants"] else "variants.called.vcf"
+
 rule hapcut2_extracthairs:
     output:
         unlinked = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.unlinked.txt"
     input:
         bam = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.bam",
-        vcf = "reference.vcf"
+        vcf = variants
     log: "hapcut2_extracthairs.log"
     shell:
          "extractHAIRS"
@@ -19,7 +21,7 @@ rule hapcut2_linkfragments:
         linked = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.linked.txt"
     input:
         bam = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.bam",
-        vcf = "reference.vcf",
+        vcf = variants,
         unlinked = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.unlinked.txt"
     log: "hapcut2_linkfragments.log"
     shell:
@@ -36,7 +38,7 @@ rule hapcut2_phasing:
         phased_vcf = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.phase.phased.VCF"
     input:
         linked = "mapped.sorted.tag.mkdup.bcmerge.mol.filt.linked.txt",
-        vcf = "reference.vcf"
+        vcf = variants
     log: "hapcut2_phasing.log"
     shell:
          "hapcut2"

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -78,17 +78,25 @@ def test_final_compressed_reads_exist(tmpdir):
         assert Path(workdir / filename).exists()
 
 
-@pytest.mark.parametrize("reference_variants", [REFERENCE_VARIANTS, "null"])
-def test_reference_variants(tmpdir, reference_variants):
+def test_link_reference_variants(tmpdir):
     workdir = tmpdir / "analysis"
     init(workdir, TESTDATA_READS)
     change_config(
         workdir / DEFAULT_CONFIG,
-        [("genome_reference", REFERENCE_GENOME), ("reference_variants", reference_variants)]
+        [("genome_reference", REFERENCE_GENOME), ("reference_variants", REFERENCE_VARIANTS)]
     )
-    target = "reference.vcf"
-    run(workdir=workdir, targets=["reference.vcf"])
-    if reference_variants != "null":
-        assert Path(workdir / target).is_symlink()
-    else:
-        assert Path(workdir / target).is_file()
+    target = "variants.reference.vcf"
+    run(workdir=workdir, targets=[target])
+    assert Path(workdir / target).is_symlink()
+
+
+def test_call_variants(tmpdir):
+    workdir = tmpdir / "analysis"
+    init(workdir, TESTDATA_READS)
+    change_config(
+        workdir / DEFAULT_CONFIG,
+        [("genome_reference", REFERENCE_GENOME), ("reference_variants", "null")]
+    )
+    target = "variants.called.vcf"
+    run(workdir=workdir, targets=[target])
+    assert Path(workdir / target).is_file()