fix channels' meta for preprocessing

Author: maxulysse

subworkflows/local/bam_applybqsr/main.nf

@@ -24,13 +24,13 @@ workflow BAM_APPLYBQSR {
         .map{ meta, cram, crai, recal, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, recal, intervals ] }
 
     // RUN APPLYBQSR
-    GATK4_APPLYBQSR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] })
+    GATK4_APPLYBQSR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] })
 
     // Gather the recalibrated cram files
     cram_to_merge = GATK4_APPLYBQSR.out.cram.map{ meta, cram -> [ groupKey(meta, meta.num_intervals), cram ] }.groupTuple()
 
     // Merge and index the recalibrated cram files
-    CRAM_MERGE_INDEX_SAMTOOLS(cram_to_merge, fasta, fasta_fai)
+    CRAM_MERGE_INDEX_SAMTOOLS(cram_to_merge, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] })
 
     cram_recal = CRAM_MERGE_INDEX_SAMTOOLS.out.cram_crai
         // Remove no longer necessary field: num_intervals

subworkflows/local/bam_applybqsr_spark/main.nf

@@ -24,13 +24,13 @@ workflow BAM_APPLYBQSR_SPARK {
         .map{ meta, cram, crai, recal, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, recal, intervals ] }
 
     // RUN APPLYBQSR SPARK
-    GATK4SPARK_APPLYBQSR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] })
+    GATK4SPARK_APPLYBQSR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] })
 
     // Gather the recalibrated cram files
     cram_to_merge = GATK4SPARK_APPLYBQSR.out.cram.map{ meta, cram -> [ groupKey(meta, meta.num_intervals), cram ] }.groupTuple()
 
     // Merge and index the recalibrated cram files
-    CRAM_MERGE_INDEX_SAMTOOLS(cram_to_merge, fasta, fasta_fai)
+    CRAM_MERGE_INDEX_SAMTOOLS(cram_to_merge, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] })
 
     cram_recal = CRAM_MERGE_INDEX_SAMTOOLS.out.cram_crai
         // Remove no longer necessary field: num_intervals

subworkflows/local/bam_baserecalibrator/main.nf

@@ -26,7 +26,7 @@ workflow BAM_BASERECALIBRATOR {
         .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
 
     // RUN BASERECALIBRATOR
-    GATK4_BASERECALIBRATOR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
+    GATK4_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
 
     // Figuring out if there is one or more table(s) from the same sample
     table_to_merge = GATK4_BASERECALIBRATOR.out.table.map{ meta, table -> [ groupKey(meta, meta.num_intervals), table ] }.groupTuple().branch{

subworkflows/local/bam_baserecalibrator_spark/main.nf

@@ -26,7 +26,7 @@ workflow BAM_BASERECALIBRATOR_SPARK {
         .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
 
     // RUN BASERECALIBRATOR SPARK
-    GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta, fasta_fai, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
+    GATK4SPARK_BASERECALIBRATOR(cram_intervals, fasta.map{ meta, it -> [ it ] }, fasta_fai.map{ meta, it -> [ it ] }, dict.map{ meta, it -> [ it ] }, known_sites, known_sites_tbi)
 
     // Figuring out if there is one or more table(s) from the same sample
     table_to_merge = GATK4SPARK_BASERECALIBRATOR.out.table.map{ meta, table -> [ groupKey(meta, meta.num_intervals), table ] }.groupTuple().branch{

subworkflows/local/bam_markduplicates/main.nf

@@ -19,7 +19,7 @@ workflow BAM_MARKDUPLICATES {
     reports  = Channel.empty()
 
     // RUN MARKUPDUPLICATES
-    GATK4_MARKDUPLICATES(bam, fasta, fasta_fai)
+    GATK4_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] })
 
     // Join with the crai file
     cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true)

subworkflows/local/bam_markduplicates_spark/main.nf

@@ -22,7 +22,7 @@ workflow BAM_MARKDUPLICATES_SPARK {
     reports = Channel.empty()
 
     // RUN MARKUPDUPLICATES SPARK
-    GATK4SPARK_MARKDUPLICATES(bam, fasta, fasta_fai, dict)
+    GATK4SPARK_MARKDUPLICATES(bam, fasta.map{ meta, fasta -> [ fasta ] }, fasta_fai.map{ meta, fasta_fai -> [ fasta_fai ] }, dict.map{ meta, dict -> [ dict ] })
 
     // Index cram
     INDEX_MARKDUPLICATES(GATK4SPARK_MARKDUPLICATES.out.output)

subworkflows/local/cram_qc_mosdepth_samtools/main.nf

@@ -18,9 +18,9 @@ workflow CRAM_QC_MOSDEPTH_SAMTOOLS {
     reports = Channel.empty()
 
     // Reports run on cram
-    SAMTOOLS_STATS(cram, fasta.map{ it -> [ [ id:'fasta' ], it ] })
+    SAMTOOLS_STATS(cram, fasta)
 
-    MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), fasta.map{ it -> [ [ id:'fasta' ], it ] })
+    MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), fasta)
 
     // Gather all reports generated
     reports = reports.mix(SAMTOOLS_STATS.out.stats)

subworkflows/local/cram_sampleqc/main.nf

@@ -1,39 +1,36 @@
 include { BAM_NGSCHECKMATE                           } from '../../../subworkflows/nf-core/bam_ngscheckmate/main'
 include { CRAM_QC_MOSDEPTH_SAMTOOLS as CRAM_QC_RECAL } from '../../../subworkflows/local/cram_qc_mosdepth_samtools/main'
+
 workflow CRAM_SAMPLEQC {
 
     take:
-    ch_cram                     // channel: [ val(meta), cram, crai ]
+    cram                        // channel: [ val(meta), cram, crai ]
     ngscheckmate_bed            // channel: [ ngscheckmate_bed ]
     fasta                       // channel: [ fasta ]
     skip_baserecalibration      // boolean:
     intervals_for_preprocessing // channel:
 
     main:
 
-    ch_versions = Channel.empty()
-    reports     = Channel.empty()
+    versions = Channel.empty()
+    reports  = Channel.empty()
 
-    if(!skip_baserecalibration){
+    if (!skip_baserecalibration) {
 
         CRAM_QC_RECAL(
-            ch_cram,
+            cram,
             fasta,
             intervals_for_preprocessing)
 
         // Gather QC reports
         reports = CRAM_QC_RECAL.out.reports.collect{ meta, report -> report }
 
         // Gather used softwares versions
-        ch_versions = ch_versions.mix(CRAM_QC_RECAL.out.versions)
+        versions = versions.mix(CRAM_QC_RECAL.out.versions)
     }
 
-    ch_ngscheckmate_bed = ngscheckmate_bed.map{bed -> [[id: "ngscheckmate"], bed]}
-
-    ch_fasta            = fasta.map{fasta -> [[id: "genome"], fasta]}
-
-    BAM_NGSCHECKMATE ( ch_cram.map{meta, cram, crai -> [meta, cram]}, ch_ngscheckmate_bed, ch_fasta)
-    ch_versions = ch_versions.mix(BAM_NGSCHECKMATE.out.versions.first())
+    BAM_NGSCHECKMATE(cram.map{meta, cram, crai -> [meta, cram]}, ngscheckmate_bed.map{bed -> [[id: "ngscheckmate"], bed]}, fasta)
+    versions = versions.mix(BAM_NGSCHECKMATE.out.versions.first())
 
     emit:
     corr_matrix  = BAM_NGSCHECKMATE.out.corr_matrix  // channel: [ meta, corr_matrix ]
@@ -43,6 +40,6 @@ workflow CRAM_SAMPLEQC {
     pdf          = BAM_NGSCHECKMATE.out.pdf          // channel: [ meta, pdf ]
     reports
 
-    versions = ch_versions                     // channel: [ versions.yml ]
+    versions // channel: [ versions.yml ]
 }
 

subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf

@@ -23,11 +23,11 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON {
     reports = Channel.empty()
 
     // Only one of the following should be run
-    BWAMEM1_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem
-    BWAMEM2_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem2
-    DRAGMAP_ALIGN(reads, index.map{ it -> [ [ id:'index' ], it ] }, [[id:'no_fasta'], []], sort) // If aligner is dragmap
+    BWAMEM1_MEM(reads, index, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem
+    BWAMEM2_MEM(reads, index, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem2
+    DRAGMAP_ALIGN(reads, index, [[id:'no_fasta'], []], sort) // If aligner is dragmap
     // The sentieon-bwamem-module does sorting as part of the conversion from sam to bam.
-    SENTIEON_BWAMEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, fasta.map{fa -> [[:], fa]}, fasta_fai.map{fai -> [[:], fai]}) // If aligner is sentieon-bwamem
+    SENTIEON_BWAMEM(reads, index, fasta, fasta_fai) // If aligner is sentieon-bwamem
 
     // Get the bam files from the aligner
     // Only one aligner is run

workflows/sarek/main.nf

@@ -637,7 +637,7 @@ workflow SAREK {
         // RUN CRAM QC on the recalibrated CRAM files or when starting from step variant calling. NGSCheckmate should be run also on non-recalibrated CRAM files
         CRAM_SAMPLEQC(cram_variant_calling,
             ngscheckmate_bed,
-            fasta.map{ meta, fasta -> [ fasta ] },
+            fasta,
             params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'),
             intervals_for_preprocessing)