Update configs

nextflowConf/biohpc.config

@@ -22,15 +22,27 @@ process {
   withName:parseMetadata {
     executor = 'local'
   }
-  withName:trimData {
+  withName:getRefERCC {
     queue = 'super'
   }
-  withName:getRefInfer {
+  withName:getRef {
+    queue = 'super'
+  }
+  withName:fastqc {
+    queue = 'super'
+  }
+  withName:seqwho {
+    executor = 'local'
+  }
+  withName:trimData {
     queue = 'super'
   }
   withName:downsampleData {
     executor = 'local'
   }
+  withName:alignSampleDataERCC {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
   withName:alignSampleData {
     queue = '128GB,256GB,256GBv1,384GB'
   }
@@ -40,9 +52,6 @@ process {
   withName:checkMetadata {
     executor = 'local'
   }
-  withName:getRef {
-    queue = 'super'
-  }
   withName:alignData {
     queue = '256GB,256GBv1'
   }
@@ -55,9 +64,6 @@ process {
   withName:makeBigWig {
     queue = 'super'
   }
-  withName:fastqc {
-    queue = 'super'
-  }
   withName:dataQC {
     queue = 'super'
   }

nextflowConf/dnanexus.config

@@ -23,12 +23,27 @@ process {
     cpus = 1
     memory = '1 GB'
   }
-  withName:trimData {
+  withName:getRefERCC {
+    machineType = 'mem1_ssd1_v2_x16'
+    cpus = 16
+    memory = '32 GB'
+  }
+  withName:getRef {
     machineType = 'mem1_ssd1_v2_x16'
     cpus = 16
     memory = '32 GB'
   }
-  withName:getRefInfer {
+  withName:fastqc {
+    machineType = 'mem1_ssd1_v2_x16'
+    cpus = 16
+    memory = '32 GB'
+  }
+  withName:seqwho {
+    executor = 'dnanexus'
+    cpus = 1
+    memory = '1 GB'
+  }
+  withName:trimData {
     machineType = 'mem1_ssd1_v2_x16'
     cpus = 16
     memory = '32 GB'
@@ -38,6 +53,9 @@ process {
     cpus = 1
     memory = '1 GB'
   }
+  withName:alignSampleDataERCC {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
   withName:alignSampleData {
     machineType = 'mem3_ssd1_v2_x16'
     cpus = 16
@@ -53,11 +71,6 @@ process {
     cpus = 1
     memory = '1 GB'
   }
-  withName:getRef {
-    machineType = 'mem1_ssd1_v2_x16'
-    cpus = 16
-    memory = '32 GB'
-  }
   withName:alignData {
     machineType = 'mem3_ssd1_v2_x32'
     cpus = 32
@@ -78,11 +91,6 @@ process {
     cpus = 16
     memory = '32 GB'
   }
-  withName:fastqc {
-    machineType = 'mem1_ssd1_v2_x16'
-    cpus = 16
-    memory = '32 GB'
-  }
   withName:dataQC {
     machineType = 'mem1_ssd1_v2_x16'
     cpus = 16
@@ -95,6 +103,8 @@ process {
   }
   withName:uploadInputBag {
     executor = 'dnanexus'
+    cpus = 1
+    memory = '1 GB'
   }
   withName:uploadExecutionRun {
     executor = 'dnanexus'

nextflowConf/multiqc_config.yaml

-custom_logo: './bicf_logo.png'
-custom_logo_url: 'https/utsouthwestern.edu/labs/bioinformatics/'
-custom_logo_title: 'Bioinformatics Core Facility'
-
-report_header_info:
-  - Contact Email: 'bicf@utsouthwestern.edu'
-  - Application Type: 'RNA-Seq Analytic Pipeline for GUDMAP/RBK'
-  - Department: 'Bioinformatic Core Facility, Department of Bioinformatics, University of Texas Southwestern Medical Center'
-
-title: RNA-Seq Analytic Pipeline for GUDMAP/RBK
-
-report_comment: >
-  This report has been generated by the <a href="https://doi.org/10.5281/zenodo.3625056">GUDMAP/RBK RNA-Seq Pipeline</a>
-
-top_modules:
-  - fastqc:
-      name: 'Raw'
-      info: 'Replicate Raw fastq QC Results'
-  - cutadapt:
-      name: 'Trim'
-      info: 'Replicate Trim Adapter QC Results'
-  - hisat2:
-      name: 'Align'
-      info: 'Replicate Alignment QC Results'
-      path_filters:
-        - '*alignSummary*'
-  - picard:
-      name: 'Dedup'
-      info: 'Replicate Alignement Deduplication QC Results'
-  - rseqc:
-      name: 'Inner Distance'
-      info: 'Replicate Paired End Inner Distance Distribution Results'
-      path_filters:
-        - '*insertSize*'
-  - custom_content
-  - featureCounts:
-      name: 'Count'
-      info: 'Replicate Feature Count QC Results'
-  - hisat2:
-      name: 'Inference: Align'
-      info: 'Inference Alignment (1M downsampled reads) QC Results'
-      path_filters:
-        - '*alignSampleSummary*'
-  - rseqc:
-      name: 'Inference: Stranded'
-      info: '1M Downsampled Reads Strandedness Inference Results'
-      path_filters:
-        - '*infer_experiment*'
-
-report_section_order:
-    run:
-      order: 4000
-    rid:
-      order: 3000
-    meta:
-      order: 2000
-    ref:
-      order: 1000
-    software_versions:
-      order: -1000
-    software_references:
-      order: -2000
-
-skip_generalstats: true
-
-custom_data:
-    run:
-        file_format: 'tsv'
-        section_name: 'Run'
-        description: 'This is the run information'
-        plot_type: 'table'
-        pconfig:
-            id: 'run'
-            scale: false
-            format: '{}'
-        headers:
-            Session:
-                description: ''
-            Session ID:
-                description: 'Nextflow session ID'
-            Pipeline Version:
-                description: 'BICF pipeline version'
-            Input:
-                description: 'Input overrides'
-    rid:
-        file_format: 'tsv'
-        section_name: 'RID'
-        description: 'This is the identifying RIDs'
-        plot_type: 'table'
-        pconfig:
-            id: 'rid'
-            scale: false
-            format: '{}'
-        headers:
-            Replicate:
-                description: ''
-            Replicate RID:
-                description: 'Replicate RID'
-            Experiment RID:
-                description: 'Experiment RID'
-            Study RID:
-                description: 'Study RID'
-    meta:
-        file_format: 'tsv'
-        section_name: 'Metadata'
-        description: 'This is the comparison of infered metadata, submitter provided, and calculated'
-        plot_type: 'table'
-        pconfig:
-            id: 'meta'
-            scale: false
-            format: '{:,.0f}'
-        headers:
-            Source:
-                description: 'Metadata source'
-            Species:
-                description: 'Species'
-            Ends:
-                description: 'Single or paired end sequencing'
-            Stranded:
-                description: 'Stranded (forward/reverse) or unstranded library prep'
-            Spike-in:
-                description: 'ERCC spike in'
-            Raw Reads:
-                description: 'Number of reads of the sequencer'
-            Assigned Reads:
-                description: 'Final reads after fintering'
-            Median Read Length:
-                description: 'Average read length'
-            Median TIN:
-                description: 'Average transcript integrity number'
-
-    ref:
-        file_format: 'tsv'
-        section_name: 'Reference'
-        description: 'This is the reference version information'
-        plot_type: 'table'
-        pconfig:
-            id: 'ref'
-            scale: false
-            format: '{}'
-        headers:
-            Species:
-                description: 'Reference species'
-            Genome Reference Consortium Build:
-                description: 'Reference source build'
-            Genome Reference Consortium Patch:
-                description: 'Reference source patch version'
-            GENCODE Annotation Release:
-                description: 'Annotation release version'
-    tin:
-        file_format: 'tsv'
-        section_name: 'TIN'
-        description: 'This is the distribution of TIN values calculated by the tool RSeQC'
-        plot_type: 'bargraph'
-        pconfig:
-            id: 'tin'
-        headers:
-            chrom
-            1 - 10
-            11 - 20
-            21 - 30
-            31 - 40
-            41 - 50
-            51 - 60
-            61 - 70
-            71 - 80
-            81 - 90
-            91 - 100
-
-sp:
-    run:
-        fn: "run.tsv"
-    rid:
-        fn: 'rid.tsv'
-    meta:
-        fn: 'metadata.tsv'
-    ref:
-        fn: 'reference.tsv'
-    tin:
-        fn: '*_tin.hist.tsv'