Fixed issue 18

Sydney-Informatics-Hub · Jul 8, 2022 · 8a56949 · 8a56949
1 parent 47ddacf
commit 8a56949
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Showing 17 changed files with 14 additions and 11 deletions.
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/align_run_parallel.pbs b/align_run_parallel.pbs
diff --git a/bqsr_apply_run_parallel.pbs b/bqsr_apply_run_parallel.pbs
diff --git a/bqsr_gather_run_parallel.pbs b/bqsr_gather_run_parallel.pbs
diff --git a/bqsr_merge_run_parallel.pbs b/bqsr_merge_run_parallel.pbs
diff --git a/bqsr_recal_make_input.sh b/bqsr_recal_make_input.sh
@@ -23,7 +23,13 @@
 
 cohort=../$1
 
-group=false
+group=true
+
+if [[ $group =~ true ]]; then
+	printf "Creating group-based BQSR recalibration inputs from ${cohort}.config\n"
+else
+	printf "Creating BQSR recalibration inputs from ${cohort}.config, no sample grouping applied\n"
+fi
 
 t_input=./Inputs/bqsr_recal.inputs-tumour
 n_input=./Inputs/bqsr_recal.inputs-normal
@@ -36,43 +42,40 @@ rm -f $input
 intervals=$(ls -1 ../Reference/BQSR_intervals/*list) #directory of text files generated by GATK SplitIntervals
 intervals=($intervals)
 
-# Collect sample IDs from samples.config
-# Only collect IDs for germline variant calling (labids ending in -B or -N)
+# Collect sample IDs from cohort.config
 while read -r sampleid labid seq_center library; do
-        if [[ ! ${sampleid} =~ ^#.*$ && ! ${labid} =~ -T.*$ && ! ${labid} =~ -P.*$ && ! ${labid} =~ -M.*$ ]]; then
+        if [[ ! ${sampleid} =~ ^#.*$ ]] 
+	then
                 if [[ $group =~ true ]]; then
-                       if [[ $labid =~ *-N|B ]]; then
+                       if [[ $labid =~ -N|-B ]]; then
                                 samples_n+=("${labid}")
-                                group_input=${n_input}
                         else
                                 samples_t+=("${labid}")
-                                group_input=${t_input}
                         fi
                 else
                         samples+=("${labid}")
-                        group_input=${input}
                 fi
         fi
 done < "${cohort}.config"
 
 for n_sample in ${samples_n[@]}; do
         for ((i=0;i<${#intervals[@]};i++))
         do
-                printf "${n_sample},${i},${intervals[i]}\n" >> ${group_input}
+                printf "${n_sample},${i},${intervals[i]}\n" >> ${n_input}
         done
 done
 
 for t_sample in ${samples_t[@]}; do
         for ((i=0;i<${#intervals[@]};i++))
         do
-                printf "${t_sample},${i},${intervals[i]}\n" >> ${group_input}
+                printf "${t_sample},${i},${intervals[i]}\n" >> ${t_input}
         done
 done
 
 for sample in ${samples[@]}; do
         for ((i=0;i<${#intervals[@]};i++))
         do
-                printf "${sample},${i},${intervals[i]}\n" >> ${group_input}
+                printf "${sample},${i},${intervals[i]}\n" >> ${input}
         done
 
 done

diff --git a/bqsr_recal_run_parallel.pbs b/bqsr_recal_run_parallel.pbs
diff --git a/bwa-postalt.js b/bwa-postalt.js
diff --git a/create_gatk_ref_intervals.pbs b/create_gatk_ref_intervals.pbs
diff --git a/dedup_sort_run_parallel.pbs b/dedup_sort_run_parallel.pbs
diff --git a/fastqc_run_parallel.pbs b/fastqc_run_parallel.pbs
diff --git a/index_reference.pbs b/index_reference.pbs
diff --git a/index_run_parallel.pbs b/index_run_parallel.pbs
diff --git a/merge_align_run_parallel.pbs b/merge_align_run_parallel.pbs
diff --git a/split_fastq_check_fastq_input_vs_split_output_run_parallel.pbs b/split_fastq_check_fastq_input_vs_split_output_run_parallel.pbs
diff --git a/split_fastq_run_parallel.pbs b/split_fastq_run_parallel.pbs