update all modules + fix path to subworkflows

modules.json

@@ -105,6 +105,11 @@
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
+                    "mosdepth": {
+                        "branch": "master",
+                        "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",

subworkflows/nf-core/align_star.nf → subworkflows/local/align_star/main.nf

@@ -2,8 +2,8 @@
 // Alignment with STAR
 //
 
-include { STAR_ALIGN        } from '../../modules/nf-core/star/align/main'
-include { BAM_SORT_SAMTOOLS } from './bam_sort_samtools'
+include { STAR_ALIGN        } from '../../../modules/nf-core/star/align/main'
+include { BAM_SORT_SAMTOOLS } from '../bam_sort_samtools/main'
 
 workflow ALIGN_STAR {
     take:

subworkflows/local/annotate.nf → subworkflows/local/annotate/main.nf

@@ -2,9 +2,9 @@
 // ANNOTATION
 //
 
-include { SNPEFF_ANNOTATE } from '../nf-core/snpeff_annotate'
-include { ENSEMBLVEP_ANNOTATE as MERGE_ANNOTATE } from '../nf-core/ensemblvep_annotate'
-include { ENSEMBLVEP_ANNOTATE } from '../nf-core/ensemblvep_annotate'
+include { SNPEFF_ANNOTATE                       } from '../snpeff_annotate/main'
+include { ENSEMBLVEP_ANNOTATE as MERGE_ANNOTATE } from '../ensemblvep_annotate/main'
+include { ENSEMBLVEP_ANNOTATE                   } from '../ensemblvep_annotate/main'
 
 workflow ANNOTATE {
     take:

subworkflows/local/bam_markduplicates/main.nf

@@ -0,0 +1,43 @@
+//
+// MARKDUPLICATES AND QC after mapping
+//
+// For all modules here:
+// A when clause condition is defined in the conf/modules.config to determine if the module should be run
+
+include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
+include { GATK4_MARKDUPLICATES      } from '../../../modules/nf-core/gatk4/markduplicates/main'
+
+workflow BAM_MARKDUPLICATES {
+    take:
+    bam                    // channel: [mandatory] [ meta, bam ]
+    fasta                  // channel: [mandatory] [ fasta ]
+    fasta_fai              // channel: [mandatory] [ fasta_fai ]
+    intervals_bed_combined // channel: [optional]  [ intervals_bed ]
+
+    main:
+    versions = Channel.empty()
+    reports  = Channel.empty()
+
+    // RUN MARKDUPLICATES
+    GATK4_MARKDUPLICATES(bam, fasta, fasta_fai)
+
+    // Join with the crai file
+    cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true)
+
+    // QC on CRAM
+    CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined)
+
+    // Gather all reports generated
+    reports = reports.mix(GATK4_MARKDUPLICATES.out.metrics)
+    reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports)
+
+    // Gather versions of all tools used
+    versions = versions.mix(GATK4_MARKDUPLICATES.out.versions)
+    versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions)
+
+    emit:
+    cram
+    reports
+
+    versions    // channel: [ versions.yml ]
+}

subworkflows/nf-core/bam_sort_samtools.nf → subworkflows/local/bam_sort_samtools/main.nf

@@ -2,9 +2,9 @@
 // Sort, index BAM file and run samtools stats, flagstat and idxstats
 //
 
-include { SAMTOOLS_SORT      } from '../../modules/nf-core/samtools/sort/main'
-include { SAMTOOLS_INDEX     } from '../../modules/nf-core/samtools/index/main'
-include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools'
+include { SAMTOOLS_SORT      } from '../../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX     } from '../../../modules/nf-core/samtools/index/main'
+include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main'
 
 workflow BAM_SORT_SAMTOOLS {
     take:

subworkflows/nf-core/bam_stats_samtools.nf → subworkflows/local/bam_stats_samtools/main.nf

@@ -2,9 +2,9 @@
 // Run SAMtools stats, flagstat and idxstats
 //
 
-include { SAMTOOLS_STATS    } from '../../modules/nf-core/samtools/stats/main'
-include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main'
-include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main'
+include { SAMTOOLS_STATS    } from '../../../modules/nf-core/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'
 
 workflow BAM_STATS_SAMTOOLS {
     take:

subworkflows/local/cram_qc_mosdepth_samtools/main.nf

@@ -0,0 +1,38 @@
+//
+// QC on CRAM
+//
+// For all modules here:
+// A when clause condition is defined in the conf/modules.config to determine if the module should be run
+
+include { SAMTOOLS_STATS     } from '../../../modules/nf-core/samtools/stats/main'
+include { MOSDEPTH           } from '../../../modules/nf-core/mosdepth/main'
+
+workflow CRAM_QC_MOSDEPTH_SAMTOOLS {
+    take:
+    cram                          // channel: [mandatory] [ meta, cram, crai ]
+    fasta                         // channel: [mandatory] [ fasta ]
+    intervals
+
+    main:
+    versions = Channel.empty()
+    reports = Channel.empty()
+
+    // Reports run on cram
+    SAMTOOLS_STATS(cram, fasta.map{ it -> [ [ id:'fasta' ], it ] })
+
+    MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), fasta.map{ it -> [ [ id:'fasta' ], it ] })
+
+    // Gather all reports generated
+    reports = reports.mix(SAMTOOLS_STATS.out.stats)
+    reports = reports.mix(MOSDEPTH.out.global_txt)
+    reports = reports.mix(MOSDEPTH.out.regions_txt)
+
+    // Gather versions of all tools used
+    versions = versions.mix(MOSDEPTH.out.versions)
+    versions = versions.mix(SAMTOOLS_STATS.out.versions.first())
+
+    emit:
+    reports
+
+    versions // channel: [ versions.yml ]
+}

subworkflows/nf-core/ensemblvep_annotate.nf → subworkflows/local/ensemblvep_annotate/main.nf

@@ -2,8 +2,8 @@
 // Run VEP to annotate VCF files
 //
 
-include { ENSEMBLVEP_VEP } from '../../modules/nf-core/ensemblvep/vep/main'
-include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { ENSEMBLVEP_VEP   } from '../../../modules/nf-core/ensemblvep/vep/main'
+include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow ENSEMBLVEP_ANNOTATE {
     take: