Merge branch 'develop' into enhancement/multiqc

assets/pipeline_multiqc_config.yml

@@ -1,12 +1,12 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/anoronh4/forte" target="_blank">anoronh4/forte</a>
+  This report has been generated by the <a href="https://github.com/mskcc/forte" target="_blank">mskcc/forte</a>
   analysis pipeline.
 report_section_order:
-  "anoronh4-forte-methods-description":
+  "mskcc-forte-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "anoronh4-forte-summary":
+  "mskcc-forte-summary":
     order: -1002
 
 export_plots: true

conf/modules.config

@@ -35,14 +35,52 @@ process {
         ]
     }
 
-    withName: '.*:QC:MULTIQC' {
+    withName: '.*:QC_DEDUP:MULTIQC_COLLECT' {
+        ext.args = {
+            [
+                "--cl-config \"subtitle: 'Deduplicated Bam'\"",
+                "-n dedupbam_multiqc_report"
+            ].join(" ")
+        }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: '.*:QC_DUP:MULTIQC_COLLECT' {
+        ext.args = {
+            [
+                "--cl-config \"subtitle: 'Non-deduplicated Bam'\"",
+                "-n dupbam_multiqc_report"
+            ].join(" ")
+        }
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*:QC_DEDUP:MULTIQC' {
+        ext.args = {
+            [
+                "--cl-config \"subtitle: 'Deduplicated Bam'\"",
+                "-n dedupbam_multiqc_report"
+            ].join(" ")
+        }
+    }
+
+    withName: '.*:QC_DUP:MULTIQC' {
+        ext.args = {
+            [
+                "--cl-config \"subtitle: 'Non-deduplicated Bam'\"",
+                "-n dupbam_multiqc_report"
+            ].join(" ")
+        }
+    }
+
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

modules.json

@@ -48,7 +48,8 @@
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",

subworkflows/local/qc.nf

@@ -2,23 +2,24 @@ ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config
 
 include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/nf-core/picard/collectrnaseqmetrics/main'
 include { PICARD_COLLECTHSMETRICS     } from '../../modules/nf-core/picard/collecthsmetrics/main'
-include { MULTIQC                     } from '../../modules/nf-core/multiqc/main'
+include {
+    MULTIQC ;
+    MULTIQC as MULTIQC_COLLECT
+} from '../../modules/nf-core/multiqc/main'
 include { BAM_RSEQC                   } from '../nf-core/bam_rseqc/main'
 
 workflow QC {
 
     take:
     bam
     bai
+    multiqc_files
     refflat
     rrna_intervals
     rseqc_bed
     fai
     dict
     baits
-    fastp_json
-    htseq_counts
-    star_log_final
 
     main:
     fasta = params.fasta
@@ -55,11 +56,9 @@ workflow QC {
         dict.map{ dict -> [[:],dict]}
     )
 
-    multiqc_ch = PICARD_COLLECTRNASEQMETRICS.out.metrics
-        .mix(fastp_json)
-<<<<<<< HEAD
-        .mix(star_log_final)
-        .mix(htseq_counts)
+    multiqc_files = multiqc_files
+        .mix(PICARD_COLLECTRNASEQMETRICS.out.metrics)
+	.mix(PICARD_COLLECTHSMETRICS.out.metrics)
         .mix(BAM_RSEQC.out.bamstat_txt)
         .mix(BAM_RSEQC.out.innerdistance_freq)
         .mix(BAM_RSEQC.out.inferexperiment_txt)
@@ -68,14 +67,19 @@ workflow QC {
         .mix(BAM_RSEQC.out.readdistribution_txt)
         .mix(BAM_RSEQC.out.readduplication_pos_xls)
         .mix(BAM_RSEQC.out.tin_txt)
-=======
-        .mix(PICARD_COLLECTHSMETRICS.out.metrics)
->>>>>>> develop
-        .map{meta, multiqc_files -> multiqc_files }
-        .collect()
+        .map{ meta, file ->
+            [meta.subMap(['sample']),file]
+        }
 
     MULTIQC(
-        multiqc_ch,
+        multiqc_files.groupTuple(by:[0]),
+        ch_multiqc_config.collect().ifEmpty([]),
+        [],
+        []
+    )
+
+    MULTIQC_COLLECT(
+        multiqc_files.map{meta, multiqc_files -> multiqc_files}.collect().map{[[:],it]},
         ch_multiqc_config.collect().ifEmpty([]),
         [],
         []

workflows/forte.nf

@@ -54,7 +54,10 @@ include { PREPROCESS_READS                  } from '../subworkflows/local/prepro
 include { ALIGN_READS                       } from '../subworkflows/local/align_reads'
 include { MERGE_READS                       } from '../subworkflows/local/merge_reads'
 include { MULTIQC                           } from '../modules/nf-core/multiqc/main'
-include { QC                                } from '../subworkflows/local/qc'
+include {
+    QC as QC_DUP ;
+    QC as QC_DEDUP
+} from '../subworkflows/local/qc'
 include { QUANTIFICATION                    } from '../subworkflows/local/quantification'
 include { FUSION                            } from '../subworkflows/local/fusion'
 
@@ -122,20 +125,34 @@ workflow FORTE {
     )
     ch_versions = ch_versions.mix(FUSION.out.ch_versions)
 
-    QC(
+    QC_DEDUP(
+        ALIGN_READS.out.bam,
+        ALIGN_READS.out.bai,
+        PREPROCESS_READS.out.fastp_json
+            .mix(QUANTIFICATION.out.htseq_counts)
+            .mix(ALIGN_READS.out.star_log_final),
+        PREPARE_REFERENCES.out.refflat,
+        PREPARE_REFERENCES.out.rrna_interval_list,
+        PREPARE_REFERENCES.out.rseqc_bed,	
+        PREPARE_REFERENCES.out.fasta_fai,
+        PREPARE_REFERENCES.out.fasta_dict,
+        BAIT_INPUTS.out.baits
+    )
+    ch_versions = ch_versions.mix(QC_DEDUP.out.ch_versions)
+
+    QC_DUP(
         ALIGN_READS.out.bam_withdup,
         ALIGN_READS.out.bai_withdup,
+        PREPROCESS_READS.out.fastp_json
+            .mix(QUANTIFICATION.out.htseq_counts)
+            .mix(ALIGN_READS.out.star_log_final),
         PREPARE_REFERENCES.out.refflat,
         PREPARE_REFERENCES.out.rrna_interval_list,
-	PREPARE_REFERENCES.out.rseqc_bed,
-	PREPARE_REFERENCES.out.fasta_fai,
-	PREPARE_REFERENCES.out.fasta_dict,
-	BAIT_INPUTS.out.baits,
-        PREPROCESS_READS.out.fastp_json,
-        QUANTIFICATION.out.htseq_counts,
-        ALIGN_READS.out.star_log_final
+        PREPARE_REFERENCES.out.rseqc_bed,
+        PREPARE_REFERENCES.out.fasta_fai,
+        PREPARE_REFERENCES.out.fasta_dict,
+        BAIT_INPUTS.out.baits
     )
-    ch_versions = ch_versions.mix(QC.out.ch_versions)
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
@@ -155,10 +172,10 @@ workflow FORTE {
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
 
-    ch_multiqc_files.collect()
+    ch_multiqc_files = ch_multiqc_files.collect().map{ files -> [[:], files] }
 
     MULTIQC (
-        ch_multiqc_files.collect(),
+        ch_multiqc_files,
         ch_multiqc_config.collect().ifEmpty([]),
         ch_multiqc_custom_config.collect().ifEmpty([]),
         ch_multiqc_logo.collect().ifEmpty([])