fix typo in dnamapping

Author: katarzyna.otylia.sikora@gmail.com

snakePipes/shared/rules/whatshap.snakefile

@@ -1,6 +1,6 @@
 def collect_bam():
     bam = "filtered_bam/{sample}.filtered.bam"
-    if pipeline == "dnamapping" and useSpikeinForNorm:
+    if pipeline == "dnamapping" and useSpikeInForNorm:
         bam = "split_bam/{sample}_host.bam"
     return(bam)
 

snakePipes/workflows/DNAmapping/DNAmapping.py

@@ -27,7 +27,7 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          "UMIDedup": False, "UMIDedupOpts": "",
                          "UMIDedupSep": "_", "UMIBarcode": False, "cutntag": False,
                          "bcPattern": "NNNNCCCCCCCC", "aligner":"Bowtie2",
-                         "pvcf": None, "useSpikeinForNorm": False, "spikeinExt": None}):
+                         "pvcf": None, "useSpikeInForNorm": False, "spikeinExt": None}):
     """
     Parse arguments from the command line.
     """
@@ -119,14 +119,14 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                           help="Phased vcf required for whatshap haplotagging. (default: '%(default)s')",
                           default=defaults["pvcf"])
 
-    optional.add_argument("--useSpikeinForNorm",
-                          dest="useSpikeinForNorm",
+    optional.add_argument("--useSpikeInForNorm",
+                          dest="useSpikeInForNorm",
                           action="store_true",
                           help="Split bam files by host and spikein genome, then scale bam coverage results by spikein-derived size factors.")
 
     optional.add_argument("--spikeinExt",
                           dest="spikeinExt",
-                          help="Extention of spikein chromosome names in the hybrid genome. Ignored if splitHybridGenome is False (default: '%(default)s') .",
+                          help="Extention of spikein chromosome names in the hybrid genome. Ignored if useSpikeInForNorm is False (default: '%(default)s') .",
                           default=defaults["spikeinExt"])
 
     return parser

snakePipes/workflows/DNAmapping/Snakefile

@@ -46,7 +46,7 @@ include: os.path.join(maindir, "shared", "tools" , "deeptools_cmds.snakefile")
 # deepTools QC
 include: os.path.join(maindir, "shared", "rules", "deepTools_qc.snakefile")
 
-if useSpikeinForNorm:
+if useSpikeInForNorm:
     include: os.path.join(maindir, "shared", "rules", "split_bam_ops_DNA_spikein.snakefile")
 
 ## MultiQC
@@ -116,7 +116,7 @@ def run_computeGCBias(GCBias):
     return(file_list)
 
 def run_splitBam_ops():
-    if useSpikeinForNorm:
+    if useSpikeInForNorm:
         file_list = expand("split_bam/{sample}_{part}.bam",sample=samples,part=part)
         file_list.append(
             [expand("split_deepTools_qc/multiBamSummary/{part}.scaling_factors.txt",part=part),

snakePipes/workflows/DNAmapping/defaults.yaml

@@ -67,6 +67,6 @@ verbose: false
 #phased vcf
 pvcf:
 #arguments related to hybrid genome alignment
-useSpikeinForNorm: False
+useSpikeInForNorm: False
 spikeinExt: "_spikein"
 spikein_bin_size: 1000

snakePipes/workflows/DNAmapping/internals.snakefile

@@ -117,7 +117,7 @@ def get_host_and_spikein_chromosomes(genome_index, spikeinEx):
                 continue
     return([hostl,spikeinl])
 
-if useSpikeinForNorm:
+if useSpikeInForNorm:
     part=['host','spikein']
     spikein_detected=check_if_spikein_genome(genome_index,spikeinExt)
     if spikein_detected:
@@ -127,5 +127,5 @@ if useSpikeinForNorm:
             k, v = next(iter(spikein_chr.items()))
             spikein_region = ":0:".join([str(k),str(v)])
     else:
-        print("\n useSpikeinForNorm was specified but no spikein genome was detected - no spikeIn chromosomes found with extention " + spikeinExt + " .\n\n")
+        print("\n useSpikeInForNorm was specified but no spikein genome was detected - no spikeIn chromosomes found with extention " + spikeinExt + " .\n\n")
         exit(1)

tests/test_jobcounts.py

@@ -578,7 +578,7 @@ def test_spikein(self, ifs):
             '--snakemakeOptions',
             SMKOPTS,
             ifs / 'org.yaml',
-            '--useSpikeinForNorm'
+            '--useSpikeInForNorm'
         ]
         print(' '.join([str(i) for i in ci]))
         _p = sp.run(ci, capture_output=True, text=True)
@@ -594,7 +594,7 @@ def test_whatshap_allelic_spikein(self, ifs):
             '--snakemakeOptions',
             SMKOPTS,
             ifs / 'org.yaml',
-            '--useSpikeinForNorm',
+            '--useSpikeInForNorm',
             '-m',
             'allelic-whatshap',
             '--phasedVcf',