Fastq_screen and fastqc overwrites result if fastq files has same name

[parlundin]

When running the qc engine for a samples the output for fastqc and fastq_screen is overwritten if identical fastq names.

As an example:

160429_ST-E00266_0089_AHLN7YCCXX/P4302_121_S3_L001_R1_001.fastq.gz
160429_ST-E00266_0089_AHLN7YCCXX/P4302_121_S3_L001_R2_001.fastq.gz
160429_ST-E00266_0090_BHLT57CCXX/P4302_121_S3_L001_R1_001.fastq.gz
160429_ST-E00266_0090_BHLT57CCXX/P4302_121_S3_L001_R2_001.fastq.gz
160510_ST-E00201_0087_BHLMHWCCXX/P4302_121_S3_L001_R1_001.fastq.gz
160510_ST-E00201_0087_BHLMHWCCXX/P4302_121_S3_L001_R2_001.fastq.gz
160523_ST-E00201_0090_BHM3CJCCXX/P4302_121_S3_L001_R1_001.fastq.gz
160523_ST-E00201_0090_BHM3CJCCXX/P4302_121_S3_L001_R2_001.fastq.gz
160527_ST-E00269_0084_AHLT2HCCXX/P4302_121_S3_L001_R1_001.fastq.gz
160527_ST-E00269_0084_AHLT2HCCXX/P4302_121_S3_L001_R2_001.fastq.gz
160520_ST-E00198_0110_AHM5FGCCXX/P4302_121_S14_L003_R1_001.fastq.gz
160520_ST-E00198_0110_AHM5FGCCXX/P4302_121_S14_L003_R2_001.fastq.gz
160520_ST-E00198_0111_BHLMGKCCXX/P4302_121_S42_L006_R1_001.fastq.gz
160520_ST-E00198_0111_BHLMGKCCXX/P4302_121_S42_L006_R2_001.fastq.gz

Here P4302_121_S3_L001_R1_001.fastq.gz occurs several times but only result from one will be present, since previous analysis will be overwritten. This due to naming convention of the output: FastQC generates P4302_121_S3_L001_R1_001_fastqc.zip and P4302_121_S3_L001_R1_001_fastqc.html. Fastq_screen generates P4302_121_S3_L001_R1_001_screen.txt. To avoid this, one solution is to generate subfolders with FC name (AHLT2HCCXX).