Remove -b flag that @mahesh-panchal correctly pointed out was the problem

Author: jfy133

main.nf

@@ -2037,12 +2037,12 @@ process pmdtools {
     """
     ## Note all `samtools view` steps ARE required for some reason
     #Run Filtering step 
-    samtools calmd -b ${bam} ${fasta} | samtools view -h - | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -Sb - > "${libraryid}".pmd.bam
+    samtools calmd ${bam} ${fasta} | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -Sb - > "${libraryid}".pmd.bam
     
     #Run Calc Range step
     ## To allow early shut off of pipe: https://github.com/nextflow-io/nextflow/issues/1564
     trap 'if [[ \$? == 141 ]]; then echo "Shutting samtools early due to -n parameter" && samtools index ${libraryid}.pmd.bam ${size}; exit 0; fi' EXIT
-    samtools calmd -b ${bam} ${fasta} | samtools view -h - | pmdtools --deamination ${platypus} --range ${params.pmdtools_range} ${treatment} ${snpcap} -n ${params.pmdtools_max_reads} > "${libraryid}".cpg.range."${params.pmdtools_range}".txt
+    samtools calmd ${bam} ${fasta} | pmdtools --deamination ${platypus} --range ${params.pmdtools_range} ${treatment} ${snpcap} -n ${params.pmdtools_max_reads} > "${libraryid}".cpg.range."${params.pmdtools_range}".txt
     
     samtools index ${libraryid}.pmd.bam ${size}
     """