moved KHMER_UNIQUEKMERS in PREPARE_GENOME subworkflow

Author: Kevin-Brockers

main.nf

@@ -65,6 +65,8 @@ workflow NFCORE_CHIPSEQ {
         params.bowtie2_index,
         params.chromap_index,
         params.star_index,
+        params.macs_gsize,
+        params.read_length
     )
 
     //
@@ -84,7 +86,8 @@ workflow NFCORE_CHIPSEQ {
         PREPARE_GENOME.out.bwa_index,
         PREPARE_GENOME.out.bowtie2_index,
         PREPARE_GENOME.out.chromap_index,
-        PREPARE_GENOME.out.star_index
+        PREPARE_GENOME.out.star_index,
+        PREPARE_GENOME.out.macs_gsize
     )
 
     emit:

subworkflows/local/prepare_genome/main.nf

@@ -22,6 +22,7 @@ include { CHROMAP_INDEX                } from '../../../modules/nf-core/chromap/
 include { GTF2BED                      } from '../../../modules/local/gtf2bed'
 include { GENOME_BLACKLIST_REGIONS     } from '../../../modules/local/genome_blacklist_regions'
 include { STAR_GENOMEGENERATE          } from '../../../modules/local/star_genomegenerate'
+include { KHMER_UNIQUEKMERS            } from '../../../modules/nf-core/khmer/uniquekmers'
 
 workflow PREPARE_GENOME {
     take:
@@ -37,6 +38,8 @@ workflow PREPARE_GENOME {
     bowtie2_index      //    file: /path/to/bowtie2/index/
     chromap_index      //    file: /path/to/chromap/index/
     star_index         //    file: /path/to/star/index/
+    macs_gsize         // integer: effective_genome_size
+    read_length        // integer: read length
 
     main:
 
@@ -195,6 +198,22 @@ workflow PREPARE_GENOME {
         }
     }
 
+    //
+    // Calculate genome size with khmer
+    //
+    ch_macs_gsize = channel.empty()
+    ch_macs_gsize = macs_gsize
+
+    if (!macs_gsize) {
+        KHMER_UNIQUEKMERS (
+            ch_fasta.map { item -> [ [:], item]},
+            read_length
+        )
+        ch_macs_gsize = KHMER_UNIQUEKMERS.out.kmers.map { meta, file ->
+        file.text.trim() }
+    }
+
+
     emit:
     fasta         = ch_fasta                  //    path: genome.fasta
     fai           = ch_fai                    //    path: genome.fai
@@ -206,4 +225,5 @@ workflow PREPARE_GENOME {
     bowtie2_index = ch_bowtie2_index          //    path: bowtie2/index/
     chromap_index = ch_chromap_index          //    path: genome.index
     star_index    = ch_star_index             //    path: star/index/
+    macs_gsize    = ch_macs_gsize             // integer: macs_gsize
 }

workflows/chipseq.nf

@@ -43,7 +43,6 @@ include { DEEPTOOLS_COMPUTEMATRIX       } from '../modules/nf-core/deeptools/com
 include { DEEPTOOLS_PLOTPROFILE         } from '../modules/nf-core/deeptools/plotprofile'
 include { DEEPTOOLS_PLOTHEATMAP         } from '../modules/nf-core/deeptools/plotheatmap'
 include { DEEPTOOLS_PLOTFINGERPRINT     } from '../modules/nf-core/deeptools/plotfingerprint'
-include { KHMER_UNIQUEKMERS             } from '../modules/nf-core/khmer/uniquekmers'
 
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -77,6 +76,7 @@ workflow CHIPSEQ {
     ch_bowtie2_index // channel: path(bowtie2/index)
     ch_chromap_index // channel: path(chromap.index)
     ch_star_index    // channel: path(star/index/)
+    ch_macs_gsize    // channel: integer(macs_gsize)
 
     main:
 
@@ -422,22 +422,6 @@ workflow CHIPSEQ {
         ch_deeptoolsplotfingerprint_multiqc = DEEPTOOLS_PLOTFINGERPRINT.out.matrix
     }
 
-    //
-    // MODULE: Calculute genome size with khmer
-    //
-    ch_macs_gsize                     = channel.empty()
-    ch_subreadfeaturecounts_multiqc   = channel.empty()
-    ch_macs_gsize = params.macs_gsize
-
-    if (!params.macs_gsize) {
-        KHMER_UNIQUEKMERS (
-            ch_fasta.map { item -> [ [:], item]},
-            params.read_length
-        )
-        ch_macs_gsize = KHMER_UNIQUEKMERS.out.kmers.map { meta, file ->
-        file.text.trim() }
-    }
-
     // Create channels: [ meta, ip_bam, control_bam ]
     ch_ip_control_bam_bai
         .map {
@@ -466,10 +450,12 @@ workflow CHIPSEQ {
     //
     //  Consensus peaks analysis
     //
-    ch_macs3_consensus_bed_lib   = channel.empty()
-    ch_macs3_consensus_txt_lib   = channel.empty()
-    ch_deseq2_pca_multiqc        = channel.empty()
-    ch_deseq2_clustering_multiqc = channel.empty()
+    ch_macs3_consensus_bed_lib        = channel.empty()
+    ch_macs3_consensus_txt_lib        = channel.empty()
+    ch_deseq2_pca_multiqc             = channel.empty()
+    ch_deseq2_clustering_multiqc      = channel.empty()
+    ch_subreadfeaturecounts_multiqc   = channel.empty()
+
     if (!params.skip_consensus_peaks) {
         // Create channels: [ antibody, [ ip_bams ], single_end_map ]
         ch_ip_control_bam