diff --git a/nextflowConf/biohpc.config b/nextflowConf/biohpc.config
index a12f2a704b3c63df9031789c2bb05d11e04d6b3a..dff28cb4ae54ee54ad63204ec8bd88e2441eb71b 100755
--- a/nextflowConf/biohpc.config
+++ b/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'
}
diff --git a/nextflowConf/dnanexus.config b/nextflowConf/dnanexus.config
index d82ff2bd07adf66caaa827a6f86d5970f20729b6..58531a418a6cc0c31c80e1f155cfe76007b98e8a 100755
--- a/nextflowConf/dnanexus.config
+++ b/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'
diff --git a/nextflowConf/multiqc_config.yaml b/nextflowConf/multiqc_config.yaml
deleted file mode 100644
index ed1375aed47a454394029e5057695b0c15babd8c..0000000000000000000000000000000000000000
--- a/nextflowConf/multiqc_config.yaml
+++ /dev/null
@@ -1,180 +0,0 @@
-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'