Merge branch 'main' of https://github.com/mskilab-org/nf-casereports

conf/base.config

@@ -28,7 +28,7 @@ process {
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        memory = { check_max( 18.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_low {
@@ -65,9 +65,9 @@ process {
         cpus            = { check_max( 12 * task.attempt, 'cpus' ) }
         memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
-    withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
+    withName: 'BWAMEM2_MEM|BWAMEM2_MEM' {
         cpus            = { check_max( 24 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 30.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 72.GB * task.attempt, 'memory' ) }
     }
     withName: 'PARABRICKS_FQ2BAM' {
         cpus            = { check_max( 24 * task.attempt, 'cpus' ) }

conf/modules/aligner.config

@@ -84,4 +84,14 @@ process {
     withName: 'MERGE_BAM' {
         ext.prefix = { "${meta.id}.sorted" }
     }
+
+
+    withName: 'CRAM_TO_BAM_FINAL' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/alignment/final/${meta.id}/" },
+            pattern: "*{bam,bai}",
+        ]
+    }
 }
+

conf/modules/recalibrate.config

@@ -18,7 +18,7 @@ process {
     withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
-            enabled: !params.save_output_as_bam,
+            enabled: params.save_mapped,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/alignment/" },
             pattern: "*cram",
@@ -30,7 +30,7 @@ process {
             ext.prefix       = { "${meta.id}.recal" }
 
             publishDir       = [
-                enabled: !params.save_output_as_bam,
+                enabled: params.save_mapped,
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
                 pattern: "*cram"
@@ -39,7 +39,7 @@ process {
 
         withName: 'MSKILABORG_NFJABBA:NFJABBA:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' {
             publishDir       = [
-                enabled: !params.save_output_as_bam,
+                enabled: params.save_mapped,
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
                 pattern: "*{recal.cram,recal.cram.crai}"
@@ -50,7 +50,7 @@ process {
         ext.prefix       = { "${meta.id}.recal" }
 
         publishDir       = [
-            enabled: params.save_output_as_bam,
+            enabled: params.save_mapped,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
             pattern: "*{recal.bam,recal.bam.bai}"

nextflow.config

@@ -48,7 +48,7 @@ params {
     fq2bam_mark_duplicates     = true                            // Whether fq2bam should mark duplicates, set false if not using fq2bam
     fq2bam_low_memory          = false                           // Set to true if using fq2bam with gpus that have <24GB memory
     optical_duplicate_pixel_distance = 2500                      // For computing optical duplicates, 2500 for NovaSeqX+
-	save_mapped                = true                            // Mapped BAMs are saved
+	save_mapped                = false                            // Mapped BAMs are saved
 	save_output_as_bam         = true                            // Output files from alignment are saved as bam by default and not as cram files
 	seq_center                 = null                            // No sequencing center to be written in read group CN field by aligner
 	seq_platform               = null                            // Default platform written in read group PL field by aligner, null by default.

tests/test_runs/full_test/params.json

@@ -6,7 +6,7 @@
     "bwa": "/gpfs/commons/home/sdider/DB/GATK/bwa/",
     "outdir": "./results",
     "pon_dryclean": "/gpfs/commons/home/tdey/data/dryclean/MONSTER_PON_RAW/MONSTER_PON_RAW_SORTED/fixed.detergent.rds",
-    "tools": "fusions",
+    "tools": "bamqc",
     "field_dryclean": "reads",
     "genome": "GATK.GRCh37",
     "email": "[email protected]"

workflows/nfcasereports.nf

@@ -368,6 +368,14 @@ inputs = inputs
 
             ch_items.meta           = ch_items.meta - ch_items.meta.subMap('lane') + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), size: 1]
 
+        } else if (ch_items.fastq_2) {
+            ch_items.meta   = ch_items.meta + [id: ch_items.meta.sample.toString()]
+            def CN         = params.seq_center ? "CN:${params.seq_center}\\t" : ''
+
+            def flowcell   = flowcellLaneFromFastq(ch_items.fastq_1)
+            def read_group = "\"@RG\\tID:${flowcell}.${ch_items.meta.sample}\\t${CN}PU:${ch_items.meta.sample}\\tSM:${ch_items.meta.patient}_${ch_items.meta.sample}\\tLB:${ch_items.meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
+
+            ch_items.meta = ch_items.meta + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), size: 1]
         } else if (ch_items.meta.lane && ch_items.bam) {
             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" : ''
@@ -1066,6 +1074,8 @@ workflow NFCASEREPORTS {
             normal_frag_cov = Channel.empty()
                 .mix(NORMAL_FRAGCOUNTER.out.fragcounter_cov)
                 .mix(fragcounter_existing_outputs.normal)
+
+            normal_frag_cov_for_merge = normal_frag_cov.map { meta, frag_cov -> [ meta.sample, meta, frag_cov ] }
         }
 
         TUMOR_FRAGCOUNTER(bam_fragcounter_status.tumor)
@@ -1074,6 +1084,8 @@ workflow NFCASEREPORTS {
             .mix(TUMOR_FRAGCOUNTER.out.fragcounter_cov)
             .mix(fragcounter_existing_outputs.tumor)
 
+        tumor_frag_cov_for_merge = tumor_frag_cov.map { meta, frag_cov -> [ meta.sample, meta, frag_cov ] }
+
         // Only need one versions because its just one program (fragcounter)
         versions = versions.mix(TUMOR_FRAGCOUNTER.out.versions)
     }
@@ -1083,15 +1095,15 @@ workflow NFCASEREPORTS {
     if (tools_used.contains("all") || tools_used.contains("dryclean")) {
         cov_dryclean_inputs = inputs
             .filter { it.dryclean_cov.isEmpty() }
-            .map { it -> [it.meta] }
+            .map { it -> [it.meta.sample, it.meta] }
             .branch{
-                normal: it[0].status == 0
-                tumor:  it[0].status == 1
+                normal: it[1].status == 0
+                tumor:  it[1].status == 1
             }
 
-        cov_dryclean_tumor_input = tumor_frag_cov
+        cov_dryclean_tumor_input = tumor_frag_cov_for_merge
             .join(cov_dryclean_inputs.tumor)
-            .map{ it -> [ it[0], it[1] ] } // meta, frag_cov
+            .map{ it -> [ it[1], it[2] ] } // meta, frag_cov
 
         dryclean_existing_outputs = inputs
             .map { it -> [it.meta, it.dryclean_cov] }
@@ -1114,15 +1126,18 @@ workflow NFCASEREPORTS {
         versions = versions.mix(TUMOR_DRYCLEAN.out.versions)
 
         if (!params.tumor_only) {
-            cov_dryclean_normal_input = normal_frag_cov
+            cov_dryclean_normal_input = normal_frag_cov_for_merge
                 .join(cov_dryclean_inputs.normal)
-                .map{ it -> [ it[0], it[1] ] } // meta, frag_cov
+                .map{ it -> [ it[1], it[2] ] } // meta, frag_cov
 
             NORMAL_DRYCLEAN(cov_dryclean_normal_input)
 
             dryclean_normal_cov = Channel.empty()
                 .mix(NORMAL_DRYCLEAN.out.dryclean_cov)
                 .mix(dryclean_existing_outputs.normal)
+
+            dryclean_normal_cov_for_merge = dryclean_normal_cov
+                .map { it -> [ it[0].patient, it[1] ] } // meta.patient, dryclean_cov
         }
     }
 
@@ -1131,22 +1146,22 @@ workflow NFCASEREPORTS {
     if (tools_used.contains("all") || tools_used.contains("cbs")) {
         cbs_inputs = inputs
             .filter { it.seg.isEmpty() || it.nseg.isEmpty() }
-            .map { it -> [it.meta] }
+            .map { it -> [it.meta.patient, it.meta] }
             .branch{
-                normal: it[0].status == 0
-                tumor:  it[0].status == 1
+                normal: it[1].status == 0
+                tumor:  it[1].status == 1
             }
 
-        cbs_tumor_input = dryclean_tumor_cov
-            .join(cbs_inputs.tumor)
-            .map{ it -> [ it[0].patient, it[0], it[1] ] } // meta.patient, meta, dryclean tumor cov
+        cbs_tumor_input = cbs_inputs.tumor
+            .join(dryclean_tumor_cov_for_merge)
+            .map{ it -> [ it[0], it[1], it[2] ] } // meta.patient, meta, dryclean tumor cov
 
         if (params.tumor_only) {
             cov_cbs = cbs_tumor_input.map { patient, meta, tumor_cov -> [ meta, tumor_cov, [] ] }
         } else {
-            cbs_normal_input = dryclean_normal_cov
-                .join(cbs_inputs.normal)
-                .map{ it -> [ it[0].patient, it[0], it[1] ] } // meta.patient, meta, dryclean normal cov
+            cbs_normal_input = cbs_inputs.normal
+                .join(dryclean_normal_cov_for_merge)
+                .map{ it -> [ it[0], it[1], it[2] ] } // meta.patient, meta, dryclean normal cov
 
             cov_cbs = cbs_tumor_input.cross(cbs_normal_input)
                 .map { tumor, normal ->
@@ -1623,7 +1638,7 @@ workflow NFCASEREPORTS {
     if (tools_used.contains("all") || tools_used.contains("fusions")) {
         fusions_inputs = inputs.filter { it.fusions.isEmpty() }.map { it -> [it.meta.patient, it.meta] }
 
-        if (tools_used.contains("non_integer_balance")) {
+        if (tools_used.contains("non_integer_balance") || tools_used.contains("all")) {
             fusions_input_non_integer_balance = non_integer_balance_balanced_gg_for_merge
                 .join(fusions_inputs)
                 .map { it -> [ it[0], it[1] ] } // meta.patient, balanced_gg