Merge branch '9-fastqc' into 'develop'

Resolve "process_fastqc"

Closes #9

See merge request !18

.gitlab-ci.yml

@@ -67,6 +67,12 @@ dedupData:
   - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - pytest -m dedupData
 
+fastqc:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz -o .
+  - pytest -m fastqc
+
 integration_se:
   stage: integration
   script:

workflow/conf/aws_ondemand.config

@@ -11,7 +11,7 @@ process {
   executor = 'awsbatch'
   queue = 'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
   cpus = 1
-  memory = '1 GB'
+  memory = '2 GB'
 
   withName:parseMetadata {
     cpus = 5
@@ -25,10 +25,13 @@ process {
   }
   withName:alignData {
     cpus = 50
-    memory = '10 GB'
+    memory = '5 GB'
   }
   withName:dedupData {
     cpus = 2
     memory = '20 GB'
   }
+  withName:fastqc {
+    memory = '5 GB'
+  }
 }
\ No newline at end of file

workflow/conf/aws_spot.config

@@ -11,7 +11,7 @@ process {
   executor = 'awsbatch'
   queue = 'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
   cpus = 1
-  memory = '1 GB'
+  memory = '2 GB'
 
   withName:parseMetadata {
     cpus = 5
@@ -25,10 +25,13 @@ process {
   }
   withName:alignData {
     cpus = 50
-    memory = '10 GB'
+    memory = '5 GB'
   }
   withName:dedupData {
     cpus = 2
     memory = '20 GB'
   }
+  withName:fastq  {
+    memory = '5 GB'
+  }
 }

workflow/conf/biohpc.config

@@ -24,6 +24,9 @@ process {
   withName: dedupData {
     queue = 'super'
   }
+  withName: fastqc {
+    queue = 'super'
+  }
 }
 
 singularity {

workflow/nextflow.config

@@ -32,6 +32,9 @@ process {
   withName: dedupData {
     container = 'bicf/picard2.21.7:2.0.0'
   }
+  withName: fastqc {
+    container = 'bicf/fastqc:2.0.0'
+  }
 }
 
 trace {

workflow/rna-seq.nf

@@ -105,6 +105,12 @@ process getData {
     """
 }
 
+// Split fastq's
+fastqs.into {
+  fastqs_trimData
+  fastqs_fastqc
+}
+
 /*
  * parseMetadata: parses metadata to extract experiment parameters
 */
@@ -239,7 +245,7 @@ process trimData {
 
   input:
     val endsManual_trimData
-    path (fastq) from fastqs
+    path (fastq) from fastqs_trimData
 
   output:
     path ("*.fq.gz") into fastqs_trimmed
@@ -303,7 +309,7 @@ process alignData {
 }
 
 /*
- *dedupReads: mark the duplicate reads, specifically focused on PCR or optical duplicates
+ *dedupData: mark the duplicate reads, specifically focused on PCR or optical duplicates
 */
 process dedupData {
   tag "${repRID}"
@@ -323,7 +329,31 @@ process dedupData {
     hostname >${repRID}.dedup.err
     ulimit -a >>${repRID}.dedup.err
 
-    #Remove duplicated reads
+    # remove duplicated reads
     java -jar /picard/build/libs/picard.jar MarkDuplicates I=${rawBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
     """
+}
+
+/*
+ *fastqc: run fastqc on untrimmed fastq's
+*/
+process fastqc {
+  tag "${repRID}"
+  publishDir "${outDir}/fastqc", mode: 'copy', pattern: "*_fastqc.zip"
+  publishDir "${logsDir}", mode: 'copy', pattern: "*.fastq.err"
+
+  input:
+    path (fastq) from fastqs_fastqc
+
+  output:
+    path ("*_fastqc.zip") into fastqc
+
+  script:
+    """
+    hostname >${repRID}.fastqc.err
+    ulimit -a >>${repRID}.fastqc.err
+
+    # run fastqc
+    fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
+    """
 }
\ No newline at end of file

workflow/tests/test_fastqc.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../../'
+
+@pytest.mark.fastqc
+def test_fastqc():
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.R1_fastqc.zip'))
\ No newline at end of file