From 07ea4fb3afabb01495d508078f40013150fc2514 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 16 Dec 2021 11:08:54 +0000
Subject: [PATCH 1/3] Update picard MarkDuplicates module

---
 modules.json                                          | 2 +-
 modules/nf-core/modules/picard/markduplicates/main.nf | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index 582e8f8c5..8e0d2fd9c 100644
--- a/modules.json
+++ b/modules.json
@@ -31,7 +31,7 @@
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "picard/markduplicates": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "0d1e21686a586447b7592e40da9b3a7cdeedf03c"
             },
             "preseq/lcextrap": {
                 "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/modules/picard/markduplicates/main.nf
index d3bf69385..3087bff4a 100644
--- a/modules/nf-core/modules/picard/markduplicates/main.nf
+++ b/modules/nf-core/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

From 425de38f62e0a968744d2dd997c9b8104d755249 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 16 Dec 2021 12:08:32 +0000
Subject: [PATCH 2/3] Re-arrange and annotate modules.config

---
 conf/modules.config | 588 +++++++++++++++++++++-----------------------
 1 file changed, 285 insertions(+), 303 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5c738c1b3..fb226e1a9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -10,6 +10,10 @@
 ----------------------------------------------------------------------------------------
 */
 
+//
+// General configuration options
+//
+
 process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
@@ -17,26 +21,28 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    // rnaseq.nf includes
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+    withName: 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
             mode: 'copy',
-            pattern: '*_versions.yml'
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    // Local Subworkflows
-    // INPUT_CHECK
-    withName: 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK' {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
             mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            pattern: '*_versions.yml'
         ]
     }
+}
+
+//
+// Genome preparation options
+//
 
-    // PREPARE_GENOME
+process {
     withName: 'GUNZIP_.*|RSEM_PREPAREREFERENCE_TRANSCRIPTS' {
         publishDir = [
             path: { "${params.outdir}/genome" },
@@ -144,36 +150,28 @@ process {
     }
 }
 
-if (!(params.skip_fastqc || params.skip_qc)) {
+if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
     process {
-        // FASTQC_UMITOOLS_TRIMGALORE
-        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
-            ext.args   = '--quiet'
+        withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
+            ext.args   = 'build=1'
+            publishDir = [
+                path: { "${params.outdir}/genome/index" },
+                mode: 'copy',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: params.save_reference
+            ]
         }
     }
 }
 
-if (params.with_umi) {
+//
+// Read QC and trimming options
+//
+
+if (!(params.skip_fastqc || params.skip_qc)) {
     process {
-        // FASTQC_UMITOOLS_TRIMGALORE
-        withName: '.*: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}'" : '',
-                ].join(' ').trim()
-            publishDir = [
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: 'copy',
-                    pattern: "*.log"
-                ],
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: 'copy',
-                    pattern: "*.fastq.gz",
-                    enabled: params.save_umi_intermeds
-                ]
-            ]
+        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
+            ext.args   = '--quiet'
         }
     }
 }
@@ -207,20 +205,34 @@ if (!params.skip_trimming) {
     }
 }
 
-if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
+if (params.with_umi) {
     process {
-        withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
-            ext.args   = 'build=1'
+        withName: '.*: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}'" : '',
+                ].join(' ').trim()
             publishDir = [
-                path: { "${params.outdir}/genome/index" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: params.save_reference
+                [
+                    path: { "${params.outdir}/umitools" },
+                    mode: 'copy',
+                    pattern: "*.log"
+                ],
+                [
+                    path: { "${params.outdir}/umitools" },
+                    mode: 'copy',
+                    pattern: "*.fastq.gz",
+                    enabled: params.save_umi_intermeds
+                ]
             ]
         }
     }
 }
 
+//
+// Contaminant removal options
+//
+
 if (!params.skip_bbsplit) {
     process {
         withName: 'NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT' {
@@ -263,6 +275,10 @@ if (params.remove_ribo_rna) {
     }
 }
 
+//
+// General alignment options
+//
+
 if (!params.skip_alignment) {
     process {
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
@@ -301,11 +317,174 @@ if (!params.skip_alignment) {
             ]
         }
     }
+
+    if (!params.skip_markduplicates) {
+        process {
+            withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
+                ext.args   = 'ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp'
+                ext.prefix = { "${meta.id}.markdup.sorted" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/picard_metrics" },
+                        mode: 'copy',
+                        pattern: '*metrics.txt'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}" },
+                        mode: 'copy',
+                        pattern: '*.bam'
+                    ]
+                ]
+            }
+
+            withName: '.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
+                ext.args   = params.bam_csi_index ? '-c' : ''
+                ext.prefix = { "${meta.id}.markdup.sorted" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    mode: 'copy',
+                    pattern: '*.{bai,csi}'
+                ]
+            }
+
+            withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: 'copy',
+                    pattern: '*.{stats,flagstat,idxstats}'
+                ]
+            }
+        }
+    }
+
+    if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
+        process {
+            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
+                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        mode: 'copy',
+                        pattern: '*.tsv'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}" },
+                        mode: 'copy',
+                        pattern: '*.bam',
+                        enabled: (
+                            params.save_align_intermeds ||
+                            params.skip_markduplicates ||
+                            params.save_umi_intermeds
+                        )
+                    ]
+                ]
+            }
+
+            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
+                ext.args   = params.bam_csi_index ? '-c' : ''
+                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    mode: 'copy',
+                    pattern: '*.{bai,csi}',
+                    enabled: (
+                        params.save_align_intermeds ||
+                        params.skip_markduplicates ||
+                        params.save_umi_intermeds
+                    )
+                ]
+            }
+
+            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: 'copy',
+                    pattern: '*.{stats,flagstat,idxstats}'
+                ]
+            }
+        }
+    }
+
+    if (!params.skip_bigwig) {
+        process {
+            withName: BEDTOOLS_GENOMECOV {
+                ext.args   = '-split -du'
+                publishDir = [
+                    path: { "${params.outdir}/bedtools/${meta.id}" },
+                    enabled: false
+                ]
+            }
+
+            withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP' {
+                ext.prefix = { "${meta.id}.clip.forward" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    enabled: false
+                ]
+            }
+
+            withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
+                ext.prefix = { "${meta.id}.forward" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/bigwig" },
+                    mode: 'copy',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP' {
+                ext.prefix = { "${meta.id}.clip.reverse" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    enabled: false
+                ]
+            }
+
+            withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
+                ext.prefix = { "${meta.id}.reverse" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/bigwig" },
+                    mode: 'copy',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
+    if (!params.skip_stringtie) {
+        process {
+            withName: STRINGTIE {
+                ext.args   = [
+                    '-v',
+                    params.stringtie_ignore_gtf ? '' : '-e'
+                ].join(' ').trim()
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/stringtie" },
+                    mode: 'copy',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
+    if (params.aligner.contains('star')) {
+        process {
+            withName: MULTIQC_TSV_FAIL_MAPPED {
+                publishDir = [
+                    path: { "${params.outdir}/multiqc" },
+                    enabled: false
+                ]
+            }
+        }
+    }
 }
 
+//
+// STAR Salmon alignment options
+//
+
 if (!params.skip_alignment && params.aligner == 'star_salmon') {
     process {
-        // ALIGN_STAR
         withName: '.*:ALIGN_STAR:STAR_ALIGN' {
             ext.args   = [
                 '--quantMode TranscriptomeSAM',
@@ -340,7 +519,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             ]
         }
 
-        // QUANTIFY_STAR_SALMON workflow
         withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
@@ -407,52 +585,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ]
             }
 
-            // DEDUP_UMI_UMITOOLS_GENOME
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: 'copy',
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}" },
-                        mode: 'copy',
-                        pattern: '*.bam',
-                        enabled: ['star_salmon','hisat2'].contains(params.aligner) && (
-                            params.save_align_intermeds ||
-                            params.skip_markduplicates ||
-                            params.save_umi_intermeds
-                        )
-                    ]
-                ]
-            }
-
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
-                ext.args   = params.bam_csi_index ? '-c' : ''
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: 'copy',
-                    pattern: '*.{bai,csi}',
-                    enabled: ['star_salmon','hisat2'].contains(params.aligner) && (
-                        params.save_align_intermeds ||
-                        params.skip_markduplicates ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: 'copy',
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-
-            // DEDUP_UMI_UMITOOLS_TRANSCRIPTOME
             withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
                 publishDir = [
@@ -499,6 +631,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
     }
 }
 
+//
+// STAR RSEM alignment options
+//
+
 if (!params.skip_alignment && params.aligner == 'star_rsem') {
     process {
         withName: '.*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION' {
@@ -558,6 +694,10 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
     }
 }
 
+//
+// HISAT2 alignment options
+//
+
 if (!params.skip_alignment && params.aligner == 'hisat2') {
     process {
         withName: '.*:ALIGN_HISAT2:HISAT2_ALIGN' {
@@ -583,218 +723,33 @@ if (!params.skip_alignment && params.aligner == 'hisat2') {
             ]
         }
     }
+}
 
-    if (params.with_umi) {
+//
+// Post-alignment QC options
+//
+
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_preseq) {
         process {
-            // DEDUP_UMI_UMITOOLS_GENOME - Duplicated here
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+            withName: PRESEQ_LCEXTRAP {
+                ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
                 publishDir = [
                     [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        path: { "${params.outdir}/${params.aligner}/preseq" },
                         mode: 'copy',
-                        pattern: '*.tsv'
+                        pattern: "*.txt"
                     ],
                     [
-                        path: { "${params.outdir}/${params.aligner}" },
+                        path: { "${params.outdir}/${params.aligner}/preseq/log" },
                         mode: 'copy',
-                        pattern: '*.bam',
-                        enabled: ['star_salmon','hisat2'].contains(params.aligner) && (
-                            params.save_align_intermeds ||
-                            params.skip_markduplicates ||
-                            params.save_umi_intermeds
-                        )
+                        pattern: "*.log"
                     ]
                 ]
             }
-
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
-                ext.args   = params.bam_csi_index ? '-c' : ''
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: 'copy',
-                    pattern: '*.{bai,csi}',
-                    enabled: ['star_salmon','hisat2'].contains(params.aligner) && (
-                        params.save_align_intermeds ||
-                        params.skip_markduplicates ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: 'copy',
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-}
-
-if (!params.skip_alignment && params.aligner.contains('star')) {
-    process {
-        withName: MULTIQC_TSV_FAIL_MAPPED {
-            publishDir = [
-                path: { "${params.outdir}/multiqc" },
-                enabled: false
-            ]
-        }
-    }
-}
-
-if (!params.skip_alignment && !params.skip_qc && !params.skip_preseq) {
-    process {
-        withName: PRESEQ_LCEXTRAP {
-            ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/preseq" },
-                    mode: 'copy',
-                    pattern: "*.txt"
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}/preseq/log" },
-                    mode: 'copy',
-                    pattern: "*.log"
-                ]
-            ]
-        }
-    }
-}
-
-if (!params.skip_alignment && !params.skip_markduplicates) {
-    process {
-        // MARK_DUPLICATES_PICARD
-        withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
-            ext.args   = 'ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp'
-            ext.prefix = { "${meta.id}.markdup.sorted" }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/picard_metrics" },
-                    mode: 'copy',
-                    pattern: '*metrics.txt'
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: 'copy',
-                    pattern: '*.bam'
-                ]
-            ]
-        }
-
-        withName: '.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
-            ext.args   = params.bam_csi_index ? '-c' : ''
-            ext.prefix = { "${meta.id}.markdup.sorted" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: 'copy',
-                pattern: '*.{bai,csi}'
-            ]
-        }
-
-        withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                mode: 'copy',
-                pattern: '*.{stats,flagstat,idxstats}'
-            ]
         }
     }
-}
-
-if (!params.skip_alignment && !params.skip_stringtie) {
-    process {
-        withName: STRINGTIE {
-            ext.args   = [
-                '-v',
-                params.stringtie_ignore_gtf ? '' : '-e'
-            ].join(' ').trim()
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/stringtie" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
-
-if (!params.skip_alignment && !params.skip_qc && !params.skip_biotype_qc && params.featurecounts_group_type) {
-    process {
-        withName: SUBREAD_FEATURECOUNTS {
-            ext.args   = [
-                '-B -C',
-                params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
-                "-t $params.featurecounts_feature_type"
-            ].join(' ').trim()
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
 
-        withName: MULTIQC_CUSTOM_BIOTYPE {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
-
-if (!params.skip_alignment && !params.skip_bigwig) {
-    process {
-        withName: BEDTOOLS_GENOMECOV {
-            ext.args   = '-split -du'
-            publishDir = [
-                path: { "${params.outdir}/bedtools/${meta.id}" },
-                enabled: false
-            ]
-        }
-
-        // BEDGRAPH_TO_BIGWIG_FORWARD
-        withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP' {
-            ext.prefix = { "${meta.id}.clip.forward" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                enabled: false
-            ]
-        }
-
-        withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
-            ext.prefix = { "${meta.id}.forward" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/bigwig" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        // BEDGRAPH_TO_BIGWIG_REVERSE
-        withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP' {
-            ext.prefix = { "${meta.id}.clip.reverse" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                enabled: false
-            ]
-        }
-
-        withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
-            ext.prefix = { "${meta.id}.reverse" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/bigwig" },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
-
-if (!params.skip_alignment && !params.skip_qc) {
     if (!params.skip_qualimap) {
         process {
             withName: QUALIMAP_RNASEQ {
@@ -841,9 +796,33 @@ if (!params.skip_alignment && !params.skip_qc) {
         }
     }
 
+    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
+        process {
+            withName: SUBREAD_FEATURECOUNTS {
+                ext.args   = [
+                    '-B -C',
+                    params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
+                    "-t $params.featurecounts_feature_type"
+                ].join(' ').trim()
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                    mode: 'copy',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            withName: MULTIQC_CUSTOM_BIOTYPE {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                    mode: 'copy',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
     if (!params.skip_rseqc && params.rseqc_modules) {
         process {
-            // RSEQC
             withName: '.*:RSEQC:RSEQC_BAMSTAT' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
@@ -972,9 +951,28 @@ if (!params.skip_alignment && !params.skip_qc) {
     }
 }
 
+if (!params.skip_multiqc) {
+    process {
+        withName: MULTIQC {
+            ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+            publishDir = [
+                path: { [
+                    "${params.outdir}/multiqc",
+                    params.skip_alignment? '' : "/${params.aligner}"
+                    ].join('') },
+                mode: 'copy',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+}
+
+//
+// Salmon pseudi-alignment options
+//
+
 if (params.pseudo_aligner == 'salmon') {
     process {
-        // QUANTIFY_SALMON workflow
         withName: '.*:QUANTIFY_SALMON:SALMON_QUANT' {
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
@@ -1027,19 +1025,3 @@ if (params.pseudo_aligner == 'salmon') {
         }
     }
 }
-
-if (!params.skip_multiqc) {
-    process {
-        withName: MULTIQC {
-            ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
-            publishDir = [
-                path: { [
-                    "${params.outdir}/multiqc",
-                    params.skip_alignment? '' : "/${params.aligner}"
-                    ].join('') },
-                mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}

From 1bfe996f815cf0e58da47d91ac947c501d4756d1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 16 Dec 2021 12:12:49 +0000
Subject: [PATCH 3/3] Fix tyop

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index fb226e1a9..bca418433 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -968,7 +968,7 @@ if (!params.skip_multiqc) {
 }
 
 //
-// Salmon pseudi-alignment options
+// Salmon pseudo-alignment options
 //
 
 if (params.pseudo_aligner == 'salmon') {