feat(homer): Add groseq subworkflow (#1492)

* feat(homer): Add groseq subworkflow

* fix(homer): Update groseq paths

* test(homer): Update groseq bam md5sums

* test(homer): Update bed process args wildcard

* test(homer): Update groseq bed md5s

* style: Run prettier

* style(homer): Align comments

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* docs(homer): Add groseq meta.yml

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

subworkflows/nf-core/homer/groseq/main.nf

@@ -0,0 +1,50 @@
+/*
+ * Identify transcripts with homer
+ */
+
+include { HOMER_MAKETAGDIRECTORY      } from '../../../../modules/homer/maketagdirectory/main'
+include { HOMER_MAKEUCSCFILE          } from '../../../../modules/homer/makeucscfile/main'
+include { HOMER_FINDPEAKS             } from '../../../../modules/homer/findpeaks/main'
+include { HOMER_POS2BED               } from '../../../../modules/homer/pos2bed/main'
+
+workflow HOMER_GROSEQ {
+    take:
+    bam   // channel: [ val(meta), [ reads ] ]
+    fasta //    file: /path/to/bwa/index/
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    /*
+    * Create a Tag Directory From The GRO-Seq experiment
+    */
+    HOMER_MAKETAGDIRECTORY ( bam, fasta )
+    ch_versions = ch_versions.mix(HOMER_MAKETAGDIRECTORY.out.versions.first())
+
+    /*
+    * Creating UCSC Visualization Files
+    */
+    HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+    ch_versions = ch_versions.mix(HOMER_MAKEUCSCFILE.out.versions.first())
+
+    /*
+    * Find transcripts directly from GRO-Seq
+    */
+    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+    ch_versions = ch_versions.mix(HOMER_FINDPEAKS.out.versions.first())
+
+    /*
+    * Convert peak file to bed file
+    */
+    HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
+    ch_versions = ch_versions.mix(HOMER_POS2BED.out.versions.first())
+
+    emit:
+    tagdir             = HOMER_MAKETAGDIRECTORY.out.tagdir // channel: [ val(meta), [ tagdir ] ]
+    bed_graph          = HOMER_MAKEUCSCFILE.out.bedGraph   // channel: [ val(meta), [ tag_dir/*ucsc.bedGraph.gz ] ]
+    peaks              = HOMER_FINDPEAKS.out.txt           // channel: [ val(meta), [ *peaks.txt ] ]
+    bed                = HOMER_POS2BED.out.bed             // channel: [ val(meta), [ *peaks.txt ] ]
+
+    versions = ch_versions                                 // channel: [ versions.yml ]
+}

subworkflows/nf-core/homer/groseq/meta.yml

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+name: homer_groseq
+description: Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
+keywords:
+  - homer
+  - groseq
+  - nascent
+modules:
+  - homer/maketagdirectory
+  - homer/makeucscfile
+  - homer/findpeaks
+  - homer/pos2bed
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - input:
+      type: list
+      description: list of BAM files, also able to take SAM and BED as input
+      pattern: "[ *.{bam/sam/bed} ]"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+output:
+  - tagdir:
+      type: directory
+      description: The "Tag Directory"
+      pattern: "*_tagdir"
+  - bedGraph:
+      type: file
+      description: The UCSC bed graph
+      pattern: "*.bedGraph.gz"
+  - peaks:
+      type: file
+      description: The found peaks
+      pattern: "*.peaks.txt"
+  - bed:
+      type: file
+      description: A BED file of the found peaks
+      pattern: "*.bed"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Emiller88"

tests/subworkflows/nf-core/homer/groseq/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_GROSEQ as HOMER_GROSEQ_BAM
+          HOMER_GROSEQ as HOMER_GROSEQ_BED } from '../../../../../subworkflows/nf-core/homer/groseq/main'
+
+workflow test_homer_groseq_bam {
+    def input = []
+    input = [[ id: 'test' ],
+            [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
+    def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    HOMER_GROSEQ_BAM ( input, fasta )
+}
+
+workflow test_homer_groseq_bed {
+    def input = []
+    input = [[ id: 'test' ],
+            [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]]
+    def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    HOMER_GROSEQ_BED ( input, fasta )
+}

tests/subworkflows/nf-core/homer/groseq/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*:HOMER_GROSEQ_BED:HOMER_MAKETAGDIRECTORY' {
+        ext.args = "-checkGC -format bed"
+    }
+
+}

tests/subworkflows/nf-core/homer/groseq/test.yml

@@ -0,0 +1,27 @@
+- name: subworkflow homer_groseq bam
+  command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bam -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
+  tags:
+    - homer
+  files:
+    - path: output/homer/test.bed
+      md5sum: 8d40034dfe22c5cf973071aa1e8d3617
+    - path: output/homer/test.bedGraph.gz
+      md5sum: de2b2f8ab90a909b8bfbe755bdaba407
+    - path: output/homer/test.peaks.txt
+      md5sum: 8d40034dfe22c5cf973071aa1e8d3617
+    - path: output/homer/versions.yml
+      md5sum: c85dee03f1afabe406a87743a4c5506d
+
+- name: subworkflow homer_groseq bed
+  command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bed -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
+  tags:
+    - homer
+  files:
+    - path: output/homer/test.bed
+      md5sum: 25e8b64946012d1c4567a04062e90fae
+    - path: output/homer/test.bedGraph.gz
+      md5sum: 2d2d1c2d3242ff74c7a922695accb9d2
+    - path: output/homer/test.peaks.txt
+      md5sum: 25e8b64946012d1c4567a04062e90fae
+    - path: output/homer/versions.yml
+      md5sum: c9b5f1248d28c216b000cba8da738455