correct path MarkDuplicates

modules/nf-core/custom/picard/markduplicates/main.nf

@@ -31,13 +31,15 @@ process PICARD_MARKDUPLICATES {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
     """
+    mv ${fasta} ${fasta.simpleName}.fasta
+
     picard \\
         -Xmx${avail_mem}M \\
         MarkDuplicates \\
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.bam \\
-        --REFERENCE_SEQUENCE $fasta \\
+        --REFERENCE_SEQUENCE ${fasta.simpleName}.fasta \\
         --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

subworkflows/local/hicstuff_sub.nf

@@ -11,7 +11,7 @@ include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
 include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
 include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
 include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
-include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/main'
+include { FILTER_PAIR } from '../../modules/local/filterbam/main'
 include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
 include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'