Made snippet input- and output files more harmonised.

rnaseq/step2_trim/snippet.sh

@@ -1,9 +1,12 @@
 #!/bin/bash
-
-# reference: http://www.usadellab.org/cms/?page=trimmomatic
+#
+# Reference: http://www.usadellab.org/cms/?page=trimmomatic
 
 
 module load Trimmomatic
+PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
+FASTQ_OUT="${PROJECT_DIRECTORY}/step2/"
+mkdir -p "${FASTQ_OUT}"
 
 
 # Adapters can be found at
@@ -11,15 +14,25 @@ module load Trimmomatic
 # But should be verified with FastQC, or in another way.
 
 
-# (Example) Paired end
+# Trimmomatic example Paired end data.
+#
+# Flags:
+# - ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the
+#                 read.
+# - SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average
+#                  quality within the window falls below a threshold.
+# - LEADING: Cut bases off the start of a read, if below a threshold quality.
+# - TRAILING: Cut bases off the end of a read, if below a threshold quality.
+# - HEADCROP: Cut the specified number of bases from the start of the read.
+# - MINLEN: Drop the read if it is below a specified length.
 java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
   -phred33 \
-  input_forward.fq.gz \
-  input_reverse.fq.gz \
-  output_forward_paired.fq.gz \
-  output_forward_unpaired.fq.gz \
-  output_reverse_paired.fq.gz \
-  output_reverse_unpaired.fq.gz \
+  sample1_R1.fastq.gz \
+  sample1_R2.fastq.gz \
+  "${FASTQ_OUT}/sample1_R1_paired.fastq.gz" \
+  "${FASTQ_OUT}/sample1_R1_unpaired.fastq.gz" \
+  "${FASTQ_OUT}/sample1_R2_paired.fastq.gz" \
+  "${FASTQ_OUT}/sample1_R2_unpaired.fastq.gz" \
   ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
   LEADING:3 \
   TRAILING:3 \
@@ -28,11 +41,11 @@ java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
   MINLEN:50
 
 
-# (Example) Single end
+# Example single end data.
 java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar SE \
   -phred33 \
-  input.fq.gz \
-  output.fq.gz \
+  sample1.fastq.gz \
+  output.fastq.gz \
   ILLUMINACLIP:TruSeq3-SE:2:30:10 \
   LEADING:3 \
   TRAILING:3 \