refactor: nf-core subworkflows install bedgraph_bedclip_bedgraphtobigwig

Author: edmundmiller

conf/modules.config

@@ -435,15 +435,15 @@ if (!params.skip_alignment) {
                 ]
             }
 
-            withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP' {
+            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
                 ext.prefix = { "${meta.id}.clip.forward" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
                     enabled: false
                 ]
             }
 
-            withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
+            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
                 ext.prefix = { "${meta.id}.forward" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/bigwig" },
@@ -452,15 +452,15 @@ if (!params.skip_alignment) {
                 ]
             }
 
-            withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP' {
+            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
                 ext.prefix = { "${meta.id}.clip.reverse" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
                     enabled: false
                 ]
             }
 
-            withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
+            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
                 ext.prefix = { "${meta.id}.reverse" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/bigwig" },

modules.json

@@ -194,6 +194,10 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "bedgraph_bedclip_bedgraphtobigwig": {
+                        "branch": "master",
+                        "git_sha": "b81a313d8fac0a82a8a4ff0de80590b2f97f11ad"
+                    },
                     "fastq_align_hisat2": {
                         "branch": "master",
                         "git_sha": "9057e75e8ac959373a72a9402130fdea2e2d1398"

subworkflows/nf-core/bedgraph_to_bigwig.nf renamed to subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf

@@ -152,8 +152,10 @@ include {
     BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
     BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME
 } from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
-include { BEDGRAPH_TO_BIGWIG as BEDGRAPH_TO_BIGWIG_FORWARD       } from '../subworkflows/nf-core/bedgraph_to_bigwig'
-include { BEDGRAPH_TO_BIGWIG as BEDGRAPH_TO_BIGWIG_REVERSE       } from '../subworkflows/nf-core/bedgraph_to_bigwig'
+include {
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE
+} from '../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -642,13 +644,13 @@ workflow RNASEQ {
         //
         // SUBWORKFLOW: Convert bedGraph to bigWig
         //
-        BEDGRAPH_TO_BIGWIG_FORWARD (
+        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD (
             BEDTOOLS_GENOMECOV.out.bedgraph_forward,
             PREPARE_GENOME.out.chrom_sizes
         )
-        ch_versions = ch_versions.mix(BEDGRAPH_TO_BIGWIG_FORWARD.out.versions)
+        ch_versions = ch_versions.mix(BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.versions)
 
-        BEDGRAPH_TO_BIGWIG_REVERSE (
+        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE (
             BEDTOOLS_GENOMECOV.out.bedgraph_reverse,
             PREPARE_GENOME.out.chrom_sizes
         )