fix typo

NYU-Molecular-Pathology · Jul 28, 2017 · f4776b8 · f4776b8
1 parent 9861176
commit f4776b8
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Showing 15 changed files with 20 additions and 15 deletions.
diff --git a/segments/align-bismark.sh b/segments/align-bismark.sh
@@ -94,10 +94,11 @@ bismark_nucstats_original="${bismark_logs_dir}/${bismark_id}${suffix_nucstats}"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bismark_bam_final" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2
+	echo "${sample},${bismark_bam_final}" >> "$samples_csv"
 	exit 1
 fi
 

diff --git a/segments/align-bowtie2-atac.sh b/segments/align-bowtie2-atac.sh
@@ -79,10 +79,11 @@ flagstat_txt="${logs_dir}/${sample}.flagstat.txt"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bam" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2
+	echo "${sample},${bam}" >> "$samples_csv"
 	exit 1
 fi
 

diff --git a/segments/align-bwa-mem.sh b/segments/align-bwa-mem.sh
@@ -72,7 +72,7 @@ bwa_flagstat="${bwa_logs_dir}/${sample}.flagstat.txt"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bam" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/align-star.sh b/segments/align-star.sh
@@ -76,7 +76,7 @@ star_prefix="${star_logs_dir}/${sample}."
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 # if final BAM exists
 if [ -s "$bam" ] ; then

diff --git a/segments/bam-dedup-bismark.sh b/segments/bam-dedup-bismark.sh
@@ -69,10 +69,11 @@ bismark_dd_report_original="${bismark_bam/%.bam/.deduplication_report.txt}"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bismark_bam_dd_final" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2
+	echo "${sample},${bismark_bam_dd_final}" >> "$samples_csv"
 	exit 1
 fi
 

diff --git a/segments/bam-dedup-sambamba.sh b/segments/bam-dedup-sambamba.sh
@@ -64,7 +64,7 @@ bam_dd_flagstat="${dedup_logs_dir}/${sample}.flagstat.txt"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bam_dd" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/bam-ra-rc-gatk.sh b/segments/bam-ra-rc-gatk.sh
@@ -103,7 +103,7 @@ gatk_rc_pdf="${gatk_logs_dir}/${sample}.pdf"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bam_ra_rc" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/bam-rg-picard.sh b/segments/bam-rg-picard.sh
@@ -57,7 +57,7 @@ bam_rg="${bam_rg_dir}/${bam_base}.bam"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$bam_rg" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/fastq-trim-trimgalore.sh b/segments/fastq-trim-trimgalore.sh
@@ -74,10 +74,11 @@ fi
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$fastq_R1_trim" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2
+	echo "${sample},${fastq_R1_trim},${fastq_R2_trim}" >> "$samples_csv"
 	exit 1
 fi
 

diff --git a/segments/fastq-trim-trimmomatic.sh b/segments/fastq-trim-trimmomatic.sh
@@ -66,10 +66,11 @@ trimmomatic_log="${trimmomatic_logs_dir}/${sample}.txt"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$fastq_R1_trim" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2
+	echo "${sample},${fastq_R1_trim},${fastq_R2_trim}" >> "$samples_csv"
 	exit 1
 fi
 

diff --git a/segments/snvs-gatk-hc.sh b/segments/snvs-gatk-hc.sh
@@ -74,7 +74,7 @@ vcf_fixed="${vcf_dir}/${sample}.vcf"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$vcf_original" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/snvs-lofreq.sh b/segments/snvs-lofreq.sh
@@ -80,7 +80,7 @@ vcf_fixed="${vcf_dir}/${sample}.vcf"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$vcf_original" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2

diff --git a/segments/snvs-mutect2.sh b/segments/snvs-mutect2.sh
@@ -85,7 +85,7 @@ vcf_fixed="${vcf_dir}/${sample_t}-${sample_n}.vcf"
 #########################
 
 
-# skip to annotation if output exits already
+# skip to annotation if output exists already
 
 annot_cmd="bash ${code_dir}/segments/annot-annovar.sh $proj_dir $sample $vcf_fixed"
 

diff --git a/segments/snvs-strelka.sh b/segments/snvs-strelka.sh
@@ -92,7 +92,7 @@ vcf_combined="${vcf_dir}/${sample_t}-${sample_n}.all.vcf"
 #########################
 
 
-# skip to annotation if output exits already
+# skip to annotation if output exists already
 
 annot_cmd="bash ${code_dir}/segments/annot-annovar.sh $proj_dir $sample $vcf_combined"
 

diff --git a/segments/species-fastqscreen.sh b/segments/species-fastqscreen.sh
@@ -60,7 +60,7 @@ fastqscreen_txt="${fastqscreen_txt/.fastq.gz/}"
 #########################
 
 
-# exit if output exits already
+# exit if output exists already
 
 if [ -s "$fastqscreen_txt" ] ; then
 	echo -e "\n $script_name SKIP SAMPLE $sample \n" >&2