Merge branch 'Check_run_post_restructure' into 'master'

Updated script/02_trimm_and_clean and adjusted scripts/procedures.sh accordingly

See merge request !4

phages/scripts/02_trimm_and_clean.sh

@@ -2,21 +2,29 @@
 
 ## VARIABLES
 
-#path=/home/enrique/work/Gandon/coevolution/phages/
+# path=/home/enrique/work/Gandon/coevolution/phages/
 path=$1
+step_name=$2
 n_threads=35
+# n_threads=$3
+
+## Maybe declaring the place where trimmomatic.jar is stored should vo to a variable
+
 
 
 ## SCRIPT
 
-mkdir -p data/trimmed/{W_seq,R_seq,Other_seq}
+mkdir -p ${path}steps/$step_name/{W_seq,R_seq,Other_seq,uniq}
 
-trimm_summary=${path}data/summary_trimm
+trimm_summary=${path}steps/$step_name/summary_trimm
 
 rm -rf ${trimm_summary}_W ${trimm_summary}_R ${trimm_summary}_Other
 touch ${trimm_summary}_W ${trimm_summary}_R ${trimm_summary}_Other
 
 
+
+
+
     ### CREATE SYMBOLIC LINKS TO SEQUENCE FILES
     ### DIIVIDED IN 3 DIRECTORIES
 
@@ -43,7 +51,9 @@ touch ${trimm_summary}_W ${trimm_summary}_R ${trimm_summary}_Other
 
 ## DO TRIMMING FOR W_SEQUENCES.
 
-for i in /home/enrique/work/Gandon/coevolution/phages/data/fastq_ln/W_seq/*_R1_*.fastq.gz
+
+
+for i in ${path}/data/fastq_ln/W_seq/*_R1_*.fastq.gz
 do
     shortname=$(basename -s _L001_R1_001.fastq.gz $i);
     echo $shortname >> ${trimm_summary}_W;
@@ -56,21 +66,21 @@ do
         -quiet \
         $i \
         ${i/_R1_/_R2_} \
-        ${path}data/trimmed/${shortname}_R1.fq.gz \
-        ${path}test_trimm/U1.fq.gz \
-        ${path}data/trimmed/${shortname}_R2.fq.gz \
-        test_trimm/U2.fq.gz \
+        ${path}steps/$step_name/${shortname}_R1.fq.gz \
+        ${path}steps/$step_name/uniq/U1.fq.gz \
+        ${path}steps/$step_name/${shortname}_R2.fq.gz \
+        ${path}steps/$step_name/uniq/U2.fq.gz \
         CROP:145 \
         HEADCROP:11 \
         SLIDINGWINDOW:2:20 \
         MINLEN:50 
     cat /tmp/tmp.trimm_summary >> ${trimm_summary}_W;
-    rm -rf ${path}test_trimm/*;
+    rm -rf ${path}steps/$step_name/uniq/*;
     echo -e '\n####' >> ${trimm_summary}_W;
 done
 
 
-for i in /home/enrique/work/Gandon/coevolution/phages/data/fastq_ln/R_seq/*_R1_*.fastq.gz
+for i in ${path}/data/fastq_ln/R_seq/*_R1_*.fastq.gz
 do
     shortname=$(basename -s _L001_R1_001.fastq.gz $i);
     echo $shortname >> ${trimm_summary}_R;
@@ -83,22 +93,22 @@ do
         -quiet \
         $i \
         ${i/_R1_/_R2_} \
-        ${path}data/trimmed/R_seq/${shortname}_R1.fq.gz \
-        ${path}test_trimm/U1.fq.gz \
-        ${path}data/trimmed/R_seq/${shortname}_R2.fq.gz \
-        test_trimm/U2.fq.gz \
+        ${path}steps/$step_name/R_seq/${shortname}_R1.fq.gz \
+        ${path}steps/$step_name/uniq/U1.fq.gz \
+        ${path}steps/$step_name/R_seq/${shortname}_R2.fq.gz \
+        ${path}steps/$step_name/uniq/U2.fq.gz \
         CROP:145 \
         HEADCROP:11 \
         SLIDINGWINDOW:2:20 \
         MINLEN:50 
     cat /tmp/tmp.trimm_summary >> ${trimm_summary}_R;
-    rm -rf ${path}test_trimm/*;
+    rm -rf ${path}steps/$step_name/uniq/*;
     echo -e '\n####' >> ${trimm_summary}_R;
 done
 
 
 
-for i in /home/enrique/work/Gandon/coevolution/phages/data/fastq_ln/Other_seq/*_R1_*.fastq.gz
+for i in ${path}data/fastq_ln/Other_seq/*_R1_*.fastq.gz
 do
     shortname=$(basename -s _L001_R1_001.fastq.gz $i);
     echo $shortname >> ${trimm_summary}_Other;
@@ -111,17 +121,17 @@ do
         -quiet \
         $i \
         ${i/_R1_/_R2_} \
-        ${path}data/trimmed/Other_seq/${shortname}_R1.fq.gz \
-        ${path}test_trimm/U1.fq.gz \
-        ${path}data/trimmed/Other_seq/${shortname}_R2.fq.gz \
-        test_trimm/U2.fq.gz \
+        ${path}steps/$step_name/Other_seq/${shortname}_R1.fq.gz \
+        ${path}steps/$step_name/uniq/U1.fq.gz \
+        ${path}steps/$step_name/Other_seq/${shortname}_R2.fq.gz \
+        ${path}steps/$step_name/uniq/U2.fq.gz \
         CROP:145 \
         HEADCROP:11 \
         SLIDINGWINDOW:2:20 \
         MINLEN:50 
     cat /tmp/tmp.trimm_summary >> ${trimm_summary}_Other;
-    rm -rf ${path}test_trimm/*;
+    rm -rf ${path}steps/$step_name/uniq/*;
     echo -e '\n####' >> ${trimm_summary}_Other;
 done
 
-
+rm -rf ${path}steps/$step_name/uniq/

phages/scripts/procedure.sh

@@ -47,7 +47,12 @@ done
 ## environment located in:
 ## ~/envs/coev/
 
+
 ###################################
 ## QUALITY CHECK 
-
 ./scripts/01_quality_check.sh  $PWD/  qc_raw_data
+
+
+###################################
+## Trimm and clean
+./scripts/02_trimm_and_clean.sh  $PWD/  trimming