getting manipulate damage from eager/dev

Author: jbv2

workflows/eager.nf

@@ -526,7 +526,7 @@ workflow EAGER {
     //
 
     if (params.run_mapdamage_rescaling || params.run_pmd_filtering || params.run_trim_bam) {
-        MANIPULATE_DAMAGE(ch_dedupped_bams, ch_fasta_for_deduplication.fasta, REFERENCE_INDEXING.out.reference, REFERENCE_INDEXING.out.pmd_masking)
+        MANIPULATE_DAMAGE(ch_dedupped_bams, ch_fasta_for_deduplication.fasta, REFERENCE_INDEXING.out.pmd_masking)
         ch_multiqc_files = ch_multiqc_files.mix(MANIPULATE_DAMAGE.out.flagstat.collect { it[1] }.ifEmpty([]))
         ch_versions = ch_versions.mix(MANIPULATE_DAMAGE.out.versions)
         ch_bams_for_library_merge = params.genotyping_source == 'rescaled' ? MANIPULATE_DAMAGE.out.rescaled : params.genotyping_source == 'pmd' ? MANIPULATE_DAMAGE.out.filtered : params.genotyping_source == 'trimmed' ? MANIPULATE_DAMAGE.out.trimmed : ch_merged_dedup_bams