Add new metadata extraction to ci

.gitlab-ci.yml

@@ -67,6 +67,8 @@ trimData:
   script:
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5F6_1M.se -j 20 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5F6_1M.pe -j 20 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
+  - readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
+  - readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
   - pytest -m trimData
 
 downsampleData:
@@ -105,6 +107,7 @@ countData:
   script:
   - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam 
   - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
+  - assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)'
   - pytest -m makeFeatureCounts
 
 makeBigWig:

workflow/rna-seq.nf

@@ -298,7 +298,7 @@ process trimData {
     hostname > ${repRID}.trimData.log
     ulimit -a >> ${repRID}.trimData.log
 
-    # trim fastq's using trim_galore
+    # trim fastq's using trim_galore and extract median read length
     echo -e "LOG: trimming ${ends}" >> ${repRID}.trimData.log
     if [ "${ends}" == "se" ]
     then
@@ -875,7 +875,8 @@ process countData {
       featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
     fi
     echo -e "LOG: counted" >> ${repRID}.countData.log
-
+    
+    # extract assigned reads
     assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)'
     echo -e \${assignedReads} > assignedReads.csv
     echo -e "LOG: assigned reads: "\${assignedReads} >> ${repRID}.countData.log
@@ -887,6 +888,12 @@ process countData {
     """
 }
 
+// Extract number of assigned reads metadata into channel
+assignedReadsInfer = Channel.create()
+inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
+  assignedReads
+)
+
 /*
  *fastqc: run fastqc on untrimmed fastq's
 */
@@ -911,12 +918,6 @@ process fastqc {
     """
 }
 
-// Extract number of assigned reads metadata into channel
-assignedReadsInfer = Channel.create()
-inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
-  assignedReads
-)
-
 /*
  *dataQC: calculate transcript integrity numbers (TIN) and bin as well as calculate innerdistance of PE replicates
 */