feat: add amber targeted panel mode

also some fixes for running whole pipeline through parabricks from fastqs

conf/base.config

@@ -70,8 +70,8 @@ process {
         memory          = { check_max( 30.GB * task.attempt, 'memory' ) }
     }
     withName: 'PARABRICKS_FQ2BAM' {
-        cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 24 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 250.GB * task.attempt, 'memory' ) }
         accelerator     = { check_max( 1 * task.attempt, 'accelerator') }
     }
     withName: 'SAMTOOLS_MERGE|SAMTOOLS_INDEX' {

modules/local/amber/main.nf

@@ -11,7 +11,7 @@ process AMBER {
     tuple val(meta), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai)
     val genome_ver
     path heterozygous_sites
-    path target_region_bed
+    tuple val(meta2), path(target_region_bed)
 
     output:
     tuple val(meta), path('amber/'), emit: amber_dir

nextflow.config

@@ -61,6 +61,9 @@ params {
 	// SV filtering (tumor only)
 	pad_junc_filter            = 1000                            // Default Padding for SV Junction filtering
 
+    // AMBER options
+    target_bed_amber = null   // pass a bed file with target regions for running AMBER on targeted sequencing sample
+
     // HetPileups options
     filter_hets      = "TRUE"
     max_depth   = 1000

subworkflows/local/bam_amber/main.nf

@@ -6,8 +6,16 @@ include { AMBER } from '../../../modules/local/amber/main'
 include { MAKE_HET_SITES } from '../../../modules/local/amber/main'
 
 //AMBER
-genome_ver = WorkflowNfcasereports.create_value_channel(params.genome_ver_amber)
-het_sites = WorkflowNfcasereports.create_file_channel(params.het_sites_amber)
+genome_ver  = WorkflowNfcasereports.create_value_channel(params.genome_ver_amber)
+het_sites   = WorkflowNfcasereports.create_file_channel(params.het_sites_amber)
+if (params.target_bed_amber != null) {
+    target_bed_input = Channel.fromPath(params.target_bed_amber)
+                        .map{ it -> [ [id: 'target_bed'], it ] }
+} else {
+    target_bed_input = Channel.value([id: 'target_bed'])
+                        .map{ meta -> [ meta, [] ] }
+}
+
 
 workflow BAM_AMBER {
     take:
@@ -22,7 +30,7 @@ workflow BAM_AMBER {
         input,
         genome_ver,
         het_sites,
-        []
+        target_bed_input // [meta, target_bed]
     )
 
     amber_dir = amber_dir.mix(AMBER.out.amber_dir)

workflows/nfcasereports.nf

@@ -362,7 +362,7 @@ inputs = inputs
             ch_items.meta   = ch_items.meta + [id: "${ch_items.meta.sample}-${ch_items.meta.lane}".toString()]
             def CN         = params.seq_center ? "CN:${params.seq_center}\\t" : ''
 
-            def flowcell   = flowcellLaneFromFastq(fastq_1)
+            def flowcell   = flowcellLaneFromFastq(ch_items.fastq_1)
             // Don't use a random element for ID, it breaks resuming
             def read_group = "\"@RG\\tID:${flowcell}.${ch_items.meta.sample}.${ch_items.meta.lane}\\t${CN}PU:${ch_items.meta.lane}\\tSM:${ch_items.meta.patient}_${ch_items.meta.sample}\\tLB:${ch_items.meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
 
@@ -872,13 +872,13 @@ workflow NFCASEREPORTS {
 
     // Post-alignment QC
     if (tools_used.contains("all") || tools_used.contains("bamqc")) {
-        bam_qc_inputs = inputs.map { it -> [it.meta.id] }
-        bam_qc_calling = alignment_bams_final
-            .join(bam_qc_inputs)
-            .map { it -> [ it[1], it[2], it[3] ] } // meta, bam, bai
+        bam_qc_inputs = inputs.map { it -> [it.meta.sample] }
+        bam_qc_calling = bam_qc_inputs
+            .join(alignment_bams_final)
+            .map { id, meta, bam, bai -> [ meta, bam, bai ] }
 
         // omit meta since it is not used in the BAM_QC
-        dict_path = dict.map{ meta, dict -> dict }
+        dict_path = dict.map{ meta, dict -> [dict] }
         BAM_QC(bam_qc_calling, dict_path)
 
         // Gather QC
@@ -891,7 +891,7 @@ workflow NFCASEREPORTS {
     if (tools_used.contains("all") || tools_used.contains("gridss")) {
 
         // Filter out bams for which SV calling has already been done
-        bam_sv_inputs = inputs.filter { it.vcf.isEmpty() }.map { it -> [it.meta.id] }
+        bam_sv_inputs = inputs.filter { it.vcf.isEmpty() }.map { it -> [it.meta.sample] }
         bam_sv_calling = alignment_bams_final
             .join(bam_sv_inputs)
             .map { it -> [ it[1], it[2], it[3] ] } // meta, bam, bai
@@ -970,7 +970,8 @@ workflow NFCASEREPORTS {
     // AMBER
     // ##############################
     if (tools_used.contains("all") || tools_used.contains("amber")) {
-        bam_amber_inputs = inputs.filter { it.hets.isEmpty() && it.amber_dir.isEmpty() }.map { it -> [it.meta.id] }
+        bam_amber_inputs = inputs.filter { it.hets.isEmpty() && it.amber_dir.isEmpty() }.map { it -> [it.meta.sample] }
+    alignment_bams_final = alignment_bams_final
         bam_amber_calling = alignment_bams_final
             .join(bam_amber_inputs)
             .map{ it -> [ it[1], it[2], it[3] ] } // meta, bam, bai
@@ -998,14 +999,14 @@ workflow NFCASEREPORTS {
         }
 
         // All tumor samples
-        bam_amber_tumor_for_crossing = bam_amber_status.tumor.map{ meta, bam, bai -> [ meta.patient, meta + [id: meta.sample], bam, bai ] }
+        bam_amber_tumor_for_crossing = bam_amber_status.tumor.map{ meta, bam, bai -> [ meta.patient, meta, bam, bai ] }
 
         if (params.tumor_only) {
             // add empty arrays to stand-in for normals
             bam_amber_pair = bam_amber_status.tumor.map{ meta, bam, bai -> [ meta + [tumor_id: meta.sample], bam, bai, [], [] ] }
         } else {
             // All normal samples
-            bam_amber_normal_for_crossing = bam_amber_status.normal.map{ meta, bam, bai -> [ meta.patient, meta + [id: meta.sample], bam, bai ] }
+            bam_amber_normal_for_crossing = bam_amber_status.normal.map{ meta, bam, bai -> [ meta.patient, meta, bam, bai ] }
             // Crossing the normal and tumor samples to create tumor and normal pairs
             bam_amber_pair = bam_amber_normal_for_crossing.cross(bam_amber_tumor_for_crossing)
                 .map { normal, tumor ->
@@ -1041,7 +1042,7 @@ workflow NFCASEREPORTS {
     // FRAGCOUNTER
     // ##############################
     if (tools_used.contains("all") || tools_used.contains("fragcounter")) {
-        bam_fragcounter_inputs = inputs.filter { it.frag_cov.isEmpty() }.map { it -> [it.meta.id] }
+        bam_fragcounter_inputs = inputs.filter { it.frag_cov.isEmpty() }.map { it -> [it.meta.sample] }
         bam_fragcounter_calling = alignment_bams_final
             .join(bam_fragcounter_inputs)
             .map{ it -> [ it[1], it[2], it[3] ] } // meta, bam, bai
@@ -1194,11 +1195,11 @@ workflow NFCASEREPORTS {
         if (params.tumor_only) {
             bam_snv_inputs = inputs
                 .filter { it.snv_somatic_vcf.isEmpty() }
-                .map { it -> [it.meta.id] }
+                .map { it -> [it.meta.sample] }
         } else {
             bam_snv_inputs = inputs
                 .filter { it.snv_somatic_vcf.isEmpty() || it.snv_germline_vcf.isEmpty() }
-                .map { it -> [it.meta.id] }
+                .map { it -> [it.meta.sample] }
         }
 
         bam_snv_calling = alignment_bams_final
@@ -1350,7 +1351,7 @@ workflow NFCASEREPORTS {
     // ##############################
     if (tools_used.contains("all") || tools_used.contains("purple")) {
         // this channel is for merging with alignment_bams_final
-        purple_inputs = inputs.filter { it.ploidy.isEmpty() }.map { it -> [it.meta.id] }
+        purple_inputs = inputs.filter { it.ploidy.isEmpty() }.map { it -> [it.meta.sample] }
         // need a channel with patient and meta for merging with rest
         purple_inputs_for_merge = inputs.filter { it.ploidy.isEmpty() }.map { it -> [it.meta.patient, it.meta] }