refactor: nf-core subworkflows install fastq_fastqc_umitools_trimgalore

Author: edmundmiller

conf/modules.config

@@ -172,15 +172,15 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
 
 if (!(params.skip_fastqc || params.skip_qc)) {
     process {
-        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
+        withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
             ext.args   = '--quiet'
         }
     }
 }
 
 if (!params.skip_trimming) {
     process {
-        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
+        withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
             ext.args   = {
                 [
                     "--fastqc_args '-t ${task.cpus}' ",
@@ -218,7 +218,7 @@ if (!params.skip_trimming) {
 
 if (params.with_umi && !params.skip_umi_extract) {
     process {
-        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
+        withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
             ext.args   = [
                     params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
                     params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',

modules.json

@@ -148,7 +148,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40"
                     },
                     "ucsc/bedclip": {
                         "branch": "master",
@@ -201,6 +201,10 @@
                     "fastq_align_hisat2": {
                         "branch": "master",
                         "git_sha": "9057e75e8ac959373a72a9402130fdea2e2d1398"
+                    },
+                    "fastq_fastqc_umitools_trimgalore": {
+                        "branch": "master",
+                        "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40"
                     }
                 }
             }

modules/nf-core/trimgalore/main.nf

@@ -143,11 +143,11 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
 //
-include { FASTQC_UMITOOLS_TRIMGALORE } from '../subworkflows/nf-core/fastqc_umitools_trimgalore'
-include { FASTQ_ALIGN_HISAT2         } from '../subworkflows/nf-core/fastq_align_hisat2/main'
-include { BAM_SORT_STATS_SAMTOOLS    } from '../subworkflows/nf-core/bam_sort_stats_samtools/main'
-include { BAM_MARKDUPLICATES_PICARD  } from '../subworkflows/nf-core/bam_markduplicates_picard/main'
-include { BAM_RSEQC                  } from '../subworkflows/nf-core/bam_rseqc/main'
+include { FASTQ_FASTQC_UMITOOLS_TRIMGALORE } from '../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main'
+include { FASTQ_ALIGN_HISAT2               } from '../subworkflows/nf-core/fastq_align_hisat2/main'
+include { BAM_SORT_STATS_SAMTOOLS          } from '../subworkflows/nf-core/bam_sort_stats_samtools/main'
+include { BAM_MARKDUPLICATES_PICARD        } from '../subworkflows/nf-core/bam_markduplicates_picard/main'
+include { BAM_RSEQC                        } from '../subworkflows/nf-core/bam_rseqc/main'
 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
@@ -230,24 +230,24 @@ workflow RNASEQ {
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters
     //
-    FASTQC_UMITOOLS_TRIMGALORE (
+    FASTQ_FASTQC_UMITOOLS_TRIMGALORE (
         ch_cat_fastq,
         params.skip_fastqc || params.skip_qc,
         params.with_umi,
         params.skip_umi_extract,
         params.skip_trimming,
         params.umi_discard_read
     )
-    ch_versions = ch_versions.mix(FASTQC_UMITOOLS_TRIMGALORE.out.versions)
+    ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions)
 
     //
     // Filter channels to get samples that passed minimum trimmed read count
     //
     ch_fail_trimming_multiqc = Channel.empty()
-    ch_filtered_reads = FASTQC_UMITOOLS_TRIMGALORE.out.reads
+    ch_filtered_reads = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads
     if (!params.skip_trimming) {
         ch_filtered_reads
-            .join(FASTQC_UMITOOLS_TRIMGALORE.out.trim_log)
+            .join(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log)
             .map {
                 meta, reads, trim_log ->
                     if (!meta.single_end) {
@@ -787,9 +787,9 @@ workflow RNASEQ {
             ch_fail_trimming_multiqc.ifEmpty([]),
             ch_fail_mapping_multiqc.ifEmpty([]),
             ch_fail_strand_multiqc.ifEmpty([]),
-            FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),
-            FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),
-            FASTQC_UMITOOLS_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),
+            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),
+            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),
+            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),
             ch_sortmerna_multiqc.collect{it[1]}.ifEmpty([]),
             ch_star_multiqc.collect{it[1]}.ifEmpty([]),
             ch_hisat2_multiqc.collect{it[1]}.ifEmpty([]),