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Added the option -w to grep in order to filter for the exact sample names in the sample_config table
sebastian-gregoricchio · Oct 18, 2024 · fcde6a6 · fcde6a6
1 parent 81ef908
commit fcde6a6
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/workflow/SPACCa_ChIPanalyses.snakefile b/workflow/SPACCa_ChIPanalyses.snakefile
@@ -427,7 +427,7 @@ rule plotFingerprint:
         mkdir -p 05_Quality_controls_and_statistics/plotFingerprint/logs
         mkdir -p 05_Quality_controls_and_statistics/plotFingerprint/quality_metrics
 
-        INPUT_ID=$(grep {params.sample} {params.sample_config_table} | cut -f 2)
+        INPUT_ID=$(grep -w {params.sample} {params.sample_config_table} | cut -f 2)
 
         $CONDA_PREFIX/bin/plotFingerprint \
         -b {input.target_bam} \
@@ -860,8 +860,8 @@ if ((eval(str(config["bam_features"]["paired_end"])) == True)):
 
             mkdir -p 04_Called_peaks/logs
 
-            INPUT_ID=$(grep {params.sample} {params.sample_config_table} | cut -f 2)
-            CALL_BROAD=$(grep {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
+            INPUT_ID=$(grep -w {params.sample} {params.sample_config_table} | cut -f 2)
+            CALL_BROAD=$(grep -w {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
 
             if [ $CALL_BROAD == "false" ]; then
                 BROAD=""
@@ -905,7 +905,7 @@ else:
             printf '\033[1;36m{params.sample}: calculating phantom peak...\\n\033[0m'
             mkdir -p 04_Called_peaks/phantom/logs
 
-            INPUT_ID=$(grep {params.sample} {params.sample_config_table} | cut -f 2)
+            INPUT_ID=$(grep -w {params.sample} {params.sample_config_table} | cut -f 2)
 
             ${{CONDA_PREFIX}}/bin/Rscript ${{CONDA_PREFIX}}/bin/run_spp.R -rf -c='{input.target_bam}' -i="01_BAM_filtered/${{INPUT_ID}}{params.input_suffix}" -savp -out={output.phantom} &> {log.out}
             """
@@ -955,8 +955,8 @@ else:
 
             mkdir -p 04_Called_peaks/logs
 
-            INPUT_ID=$(grep {params.sample} {params.sample_config_table} | cut -f 2)
-            CALL_BROAD=$(grep {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
+            INPUT_ID=$(grep -w {params.sample} {params.sample_config_table} | cut -f 2)
+            CALL_BROAD=$(grep -w {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
 
             if [ $CALL_BROAD == "false" ]; then
                 BROAD=""
@@ -1276,7 +1276,7 @@ if ((eval(str(config["bam_features"]["paired_end"])) == True)):
             mkdir -p 05_Quality_controls_and_statistics/peaks_stats/
 
             # define peak file
-            CALL_BROAD=$(grep {params.target} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
+            CALL_BROAD=$(grep -w {params.target} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
 
             if [ $CALL_BROAD == "false" ]; then
                 CALLING_MODE="narrow"
@@ -1360,7 +1360,7 @@ else:
             mkdir -p 05_Quality_controls_and_statistics/peaks_stats/
 
             # define peak file
-            CALL_BROAD=$(grep {params.target} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
+            CALL_BROAD=$(grep -w {params.target} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
 
             if [ $CALL_BROAD == "false" ]; then
                 CALLING_MODE="narrow"
@@ -2280,7 +2280,7 @@ rule CopywriteR:
         rm -r {params.outdir}/CNAprofiles
         mkdir -p {params.outdir}
 
-        BROAD=$(grep {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
+        BROAD=$(grep -w {params.sample} {params.sample_config_table} | cut -f 3 | sed -e 's/\\(.*\\)/\\L\\1/')
 
         if [ $BROAD == "false" ]; then
             EXT="narrowPeak"