Add Percent GC

README.md

@@ -42,3 +42,4 @@ The output file includes the following headers:
 - `total_bases`
 - `average_base_quality`
 - `percent_bases_above_q30`
+- `percent_gc`

modules/combine_qc_stats.nf

@@ -15,7 +15,7 @@ process combine_qc_stats {
   printf "sample_id\\n${sample_id}\\n" > sample_id.csv
   awk -F ',' 'BEGIN {OFS=FS}; NR==1 { for (i=1; i<=NF; i++) {idx[\$i] = i} }; { print \$(idx["abundance_1_name"]), \$(idx["abundance_1_fraction_total_reads"]) }' ${species_abundance} | sed -s 's/abundance_1/most_abundant_species/g' > species_abundance_stats.csv
   awk -F ',' 'BEGIN {OFS=FS}; NR==1 { for (i=1; i<=NF; i++) {idx[\$i] = i} }; { print \$(idx["estimated_genome_size_bp"]), \$(idx["estimated_depth_coverage"]) }' ${estimated_coverage} > estimated_coverage_stats.csv
-  awk -F ',' 'BEGIN {OFS=FS}; NR==1 { for (i=1; i<=NF; i++) {idx[\$i] = i} }; { print \$(idx["total_bases"]), \$(idx["average_base_quality"]), \$(idx["percent_bases_above_q${params.seqtk_fqchk_threshold}"]) }' ${sequence_quality} > sequence_quality_stats.csv
+  awk -F ',' 'BEGIN {OFS=FS}; NR==1 { for (i=1; i<=NF; i++) {idx[\$i] = i} }; { print \$(idx["total_bases"]), \$(idx["average_base_quality"]), \$(idx["percent_bases_above_q${params.seqtk_fqchk_threshold}"]), \$(idx["percent_gc"]) }' ${sequence_quality} > sequence_quality_stats.csv
   paste -d ',' sample_id.csv species_abundance_stats.csv estimated_coverage_stats.csv sequence_quality_stats.csv > ${sample_id}_combined_qc_stats.csv
   """
 }