Made snippet input- and output files more harmonised.

rnaseq/step2_trim/snippet.sh

@@ -29,10 +29,10 @@ java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
   -phred33 \
   sample1_R1.fastq.gz \
   sample1_R2.fastq.gz \
-  "${FASTQ_OUT}/sample1_forward_paired.fastq.gz" \
-  "${FASTQ_OUT}/sample1_forward_unpaired.fastq.gz" \
-  "${FASTQ_OUT}/sample1_reverse_paired.fastq.gz" \
-  "${FASTQ_OUT}/sample1_reverse_unpaired.fastq.gz" \
+  "${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 \

rnaseq/step3_align/snippet.sh

@@ -41,9 +41,9 @@ STAR \
 # - We are assuming paired-end, gzip compressed (--readFilesCommand zcat)  FastQ
 #   files.
 
-# The compressed paired-end FastQ's that we are aligning.
-R1="sample1_R1.fastq.gz"
-R2="sample1_R2.fastq.gz"
+# The compressed, paired-end, FastQ's after trimming (step 2).
+R1="${PROJECT_DIRECTORY}/step2/sample1_R1_paired.fastq.gz"
+R2="${PROJECT_DIRECTORY}/step2/sample1_R2_paired.fastq.gz"
 
 STAR \
     --runThreadN 8 \