Added helper commands

Author: DanHUMassMed

.gitignore

@@ -7,6 +7,7 @@
 **/__pycache__
 
 # Files to ignore
+found*.sh
 docs/overview.pdf
 .nextflow.log*
 .nextflow.pid

cut_tag_trial/cleanup_work.sh

@@ -0,0 +1 @@
+rm -rf ./work/53/47afd96a82ddcdccd62a89fe56ac8c

cut_tag_trial/conf/experiment.config

@@ -1,21 +1,29 @@
 
 
 params {
-    data_remote = "cut_tag_trial"
-    experiment  = "cut_tag_trial"
+    // TODO: Add back code to pull data
+    //data_remote = "cut_tag_trial"
+    //experiment  = "cut_tag_trial"
 
-    run_get_dropbox_data       = false
-    run_fastqc                 = false
-    run_trim_galore            = false
 
-    run_cut_and_tag            = true
+    save_reference       = true
+    save_chromsize       = true //Save 
+    save_trimmed         = true //Save fastq.gz after trimming
 
+    // Alignment
+    save_unaligned       = true // Save fastq.gz before alignment
+    save_align_target    = true
+    save_align_spikein   = true
 
-    fastq_paired = "${launchDir}/data/fastq/*_R{1,2}.fastq.gz"
 
+    // Deduplication 
+    dedup_target_reads   = true
+    save_markdup_bam     = true
+    save_dedup_bam       = true
+    
 
-    genome = 'WBcel235'
+    //genome = 'WBcel235'
     //genome = 'ce10'
     sample_sheet = "${launchDir}/conf/samplesheet.csv" 
 
-}
+}

cut_tag_trial/nf-core/search.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
-SEARCH="BOWTIE2_TARGET"
-rm found*.sh
+SEARCH="$1"
+echo ${SEARCH}
+rm -f found*.sh
 count=1
 for d in `find ./work -name .command.sh`;
 do 

cut_tag_trial/run.sh

@@ -1,2 +1,3 @@
 #!/bin/bash
-nextflow -c conf/experiment.config run ../../Cut-and-Tag-Nextflow -resume -bg -with-tower -N [email protected]
+#nextflow -c conf/experiment.config run ../../Cut-and-Tag-Nextflow --save_reference true -resume -bg -with-tower -N [email protected]
+nextflow  -c conf/experiment.config run ../../Cut-and-Tag-Nextflow -resume -bg -with-tower -N [email protected]

cut_tag_trial/run_singularity.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+COMMAND=$1
+SINGULARITY_HOME=/home/daniel.higgins-umw/.singularity
+CONTAINER=danhumassmed-picard-trimmomatic-1.0.1.img
+singularity exec ${SINGULARITY_HOME}/${CONTAINER} ${COMMAND}

cut_tag_trial/search_command.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+# CHECK COMMANDLINE PARAMS
+if [ -n "$1" ]; then
+    SEARCH="$1"
+else
+    echo "Search criteria is required"
+    exit 1
+fi
+
+if [ -n "$2" ]; then
+    echo "Setting file name to .command.run"
+    FILE_NM=".command.run"
+else
+    echo "Setting file name to .command.sh"
+    FILE_NM=".command.sh"
+fi
+
+if [ "$FILE_NM" = ".command.run" ]; then
+    SEARCH="^# NEXTFLOW TASK:.*${SEARCH}"
+fi
+
+# SETUP RUN
+rm -f found*.txt
+rm -f cleanup_work.sh
+touch cleanup_work.sh
+chmod +x cleanup_work.sh
+
+count=1
+for d in `find ./work -name ${FILE_NM}`;
+do 
+    found=`cat $d|grep "${SEARCH}"`;
+    if [ -n "$found" ];
+    then
+        echo $d;
+        echo $found;
+        echo "rm -rf `dirname $d`" >>cleanup_work.sh
+        cat $d > found${count}.sh;
+        line_to_insert="# cd `dirname $d`"
+        sed -i "2i\\$line_to_insert" found${count}.sh
+        count=$((count + 1))
+    fi
+done
+