From 6f8af8c29a7a19b5370846e6f9358067eb8f7b71 Mon Sep 17 00:00:00 2001
From: kdelange <kimatwork01@gmail.com>
Date: Tue, 15 Jan 2019 13:30:35 +0100
Subject: [PATCH 1/2] script to make sample sheet for inhouse research samples

---
 makeSamplesheet_inhouse_research.sh | 195 ++++++++++++++++++++++++++++
 1 file changed, 195 insertions(+)
 create mode 100755 makeSamplesheet_inhouse_research.sh

diff --git a/makeSamplesheet_inhouse_research.sh b/makeSamplesheet_inhouse_research.sh
new file mode 100755
index 0000000..d529791
--- /dev/null
+++ b/makeSamplesheet_inhouse_research.sh
@@ -0,0 +1,195 @@
+#!/bin/bash
+
+set -e
+set -u
+
+
+function showHelp() {
+    #
+    # Display commandline help on STDOUT.
+    #
+    cat <<EOH
+===============================================================================================================
+Usage:
+        $(basename $0) OPTIONS
+        
+Options:    
+        --h  Show this help.
+
+        Required:
+        -p  projectName
+        -d  sequencingStartDate (YYMMDD)
+        -r  run (run number contains 4 numbers: 0123)
+        -f  flowcell (example: NextSeq, AHLJ5YAFXX or MiSeq, 000000000-BPJ2D_projectName)
+        -q  sequencer (NextSeq:NB501043/NB501093 or MiSeq:M01785/M01997)
+        -l  lane (number of lanes used, 1 for MiSeq, 4 for NextSeq)
+        
+        Optional:
+        -w  workDir (default is this directory)
+        -b  barcodeType (default: RPI. AGI,LEX, NEB enz.)
+        -c  capturingKit (default:None, name of capturingKit (e.g. Agilent\/ONCO_v3)
+        -k  prepKit (default:Exceptional Prep kit. Important for RNA: lexogen, TruSeq, RiboZero)
+        -g  species (default:homo_sapiens|GRCh37, if other species, supply like 'homo_sapiens|GRCh37')
+        -s  sampleType (DNA/RNA, default:RNA)
+        -t  seqType (default:PE. otheriwse specify SR)
+        -i  informationFile (default:None. Comma separated txt file, 1st column barcode, 2nd colum externaSampleID. NO HEADER!)
+        -n  SampleNumber (Numer of samples in the pool, only neseccary if no informationFile is provided)
+        
+Output will be written in workDir with the name: {projectName}.csv
+===============================================================================================================
+EOH
+    trap - EXIT
+    exit 0
+}
+sequencingStartdate=
+while getopts "w:s:k:t:g:q:l:m:p:c:d:r:f:b:n:i:h" opt;
+do
+
+    case $opt in h)showHelp;; 
+                 w)workDir="${OPTARG}";; 
+                 s)sampleType="${OPTARG}";; 
+                 k)prepKit="${OPTARG}";; 
+                 t)seqType="${OPTARG}";; 
+                 g)species="${OPTARG}";; 
+                 q)sequencer="${OPTARG}";; 
+                 l)lane="${OPTARG}";; 
+                 p)projectName="${OPTARG}";; 
+                 c)capturingKit="${OPTARG}";; 
+                 d)sequencingStartDate="${OPTARG}";; 
+                 r)run="${OPTARG}";; 
+                 f)flowcell="${OPTARG}";; 
+                 b)barcodeType="${OPTARG}";; 
+                 n)SampleNumber="${OPTARG}";;
+                 i)informationFile="${OPTARG}";;
+    esac
+done
+
+
+
+if [[ -z "${sampleType:-}" ]]; then
+    sampleType="RNA"
+fi
+
+if [[ -z "${capturingKit:-}" ]]; then
+    capturingKit="None"
+fi
+
+if [[ -z "${projectName:-}" ]]; then
+    echo -e '\nERROR: Must specify a projectName\n'
+    exit 1
+fi
+
+if [[ -z "${sequencingStartDate:-}" ]]; then
+    echo -e '\n ERROR: must specify sequencingStartDate YYMMDD'
+    exit 1
+fi
+
+if [[ -z "${seqType:-}" ]]; then
+    seqType="PE"
+fi
+
+if [[ -z "${prepKit:-}" ]]; then
+    prepKit="'Exceptional Prep kit'"
+fi
+
+if [[ -z "${workDir:-}" ]]; then
+    workDir=$(pwd)
+fi
+
+if [[ -z "${species:-}" ]]; then
+    species="homo_sapiens|GRCh37"
+fi
+
+if [[ -z "${sequencer:-}" ]]; then
+    echo -e '\n ERROR: must specify sequencer used'
+    exit 1
+fi
+
+if [[ -z "${run:-}" ]]; then
+    echo -e '\n ERROR: must specify run number, like 0123'
+    exit 1
+fi
+
+if [[ -z "${lane:-}" ]]; then
+    echo -e '\n ERROR: must specify numbers of lanes used'
+    exit 1
+fi
+
+if [[ -z "${flowcell:-}" ]]; then
+    echo -e '\n ERROR: must specify flowcell number'
+    exit 1
+fi
+
+if [[ -z "${barcodeType:-}" ]]; then
+    seqType="RPI"
+fi
+
+if [[ -z "${SampleNumber:-}" ]]; then
+    SampleNumer=""
+fi
+
+if [[ -z "${informationFile:-}" ]]; then
+    informationFile="None"
+fi
+
+
+printf "externalSampleID,barcode,project,capturingKit,sampleType,seqType,prepKit,species,Gender,arrayFile,lane,sequencingStartDate,sequencer,run,flowcell\n" > "${workDir}/${projectName}.csv"
+
+
+if [ "${informationFile}" == "None" ]; then
+    for ((l=1;l<="${lane}";l++))
+        do
+        for ((i=1;i<="${SampleNumber}";i++))
+            do
+            printf "${projectName}_sample${i}" >> "${workDir}/${projectName}.csv"  ##Dummy external sample ID
+            printf ",DummyBarcode${i}" >> "${workDir}/${projectName}.csv" ## Dummy barcode
+            printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
+            printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
+            printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
+            printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
+            printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
+            printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
+            printf "," >> "${workDir}/${projectName}.csv"  ## Gender
+            printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
+            printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
+            printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
+            printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
+            printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
+            printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
+            done
+        done
+        
+else    
+    for ((l=1;l<="${lane}";l++))
+        do
+        while read line
+            do
+            barcode=$(echo "${line}" | cut -d , -f1)
+            externaSampleID=$(echo "${line}" | cut -d , -f2)
+            printf "${externaSampleID}" >> "${workDir}/${projectName}.csv"  ##external sample ID
+            printf ",${barcode}" >> "${workDir}/${projectName}.csv" ## barcode
+            printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
+            printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
+            printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
+            printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
+            printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
+            printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
+            printf "," >> "${workDir}/${projectName}.csv"  ## Gender
+            printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
+            printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
+            printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
+            printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
+            printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
+            printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
+            done < "${informationFile}"
+        done
+fi
+
+
+echo "Samplesheet is finished!"
+
+
+
+
+
+

From 95a642fe486e1173eaa7e53a3ad5e356385100c7 Mon Sep 17 00:00:00 2001
From: kdelange <kimatwork01@gmail.com>
Date: Tue, 15 Jan 2019 15:24:19 +0100
Subject: [PATCH 2/2] changed comments makesamplesheet_inhouse_research.sh

---
 makeSamplesheet_inhouse_research.sh | 92 ++++++++++++++---------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/makeSamplesheet_inhouse_research.sh b/makeSamplesheet_inhouse_research.sh
index d529791..d782f9c 100755
--- a/makeSamplesheet_inhouse_research.sh
+++ b/makeSamplesheet_inhouse_research.sh
@@ -31,9 +31,9 @@ Options:
         -k  prepKit (default:Exceptional Prep kit. Important for RNA: lexogen, TruSeq, RiboZero)
         -g  species (default:homo_sapiens|GRCh37, if other species, supply like 'homo_sapiens|GRCh37')
         -s  sampleType (DNA/RNA, default:RNA)
-        -t  seqType (default:PE. otheriwse specify SR)
-        -i  informationFile (default:None. Comma separated txt file, 1st column barcode, 2nd colum externaSampleID. NO HEADER!)
-        -n  SampleNumber (Numer of samples in the pool, only neseccary if no informationFile is provided)
+        -t  seqType (default:PE. otherwise specify SR)
+        -i  informationFile (default:None. Comma separated txt file, 1st column barcode, 2nd colum externalSampleID. NO HEADER!)
+        -n  sampleNumber (Number of samples in the pool, only necessary if no informationFile is provided)
         
 Output will be written in workDir with the name: {projectName}.csv
 ===============================================================================================================
@@ -59,7 +59,7 @@ do
                  r)run="${OPTARG}";; 
                  f)flowcell="${OPTARG}";; 
                  b)barcodeType="${OPTARG}";; 
-                 n)SampleNumber="${OPTARG}";;
+                 n)sampleNumber="${OPTARG}";;
                  i)informationFile="${OPTARG}";;
     esac
 done
@@ -121,11 +121,11 @@ if [[ -z "${flowcell:-}" ]]; then
 fi
 
 if [[ -z "${barcodeType:-}" ]]; then
-    seqType="RPI"
+    barcodeType="RPI"
 fi
 
-if [[ -z "${SampleNumber:-}" ]]; then
-    SampleNumer=""
+if [[ -z "${sampleNumber:-}" ]]; then
+    sampleNumber=""
 fi
 
 if [[ -z "${informationFile:-}" ]]; then
@@ -138,51 +138,51 @@ printf "externalSampleID,barcode,project,capturingKit,sampleType,seqType,prepKit
 
 if [ "${informationFile}" == "None" ]; then
     for ((l=1;l<="${lane}";l++))
-        do
+    do
         for ((i=1;i<="${SampleNumber}";i++))
-            do
-            printf "${projectName}_sample${i}" >> "${workDir}/${projectName}.csv"  ##Dummy external sample ID
-            printf ",DummyBarcode${i}" >> "${workDir}/${projectName}.csv" ## Dummy barcode
-            printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
-            printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
-            printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
-            printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
-            printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
-            printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
-            printf "," >> "${workDir}/${projectName}.csv"  ## Gender
-            printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
-            printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
-            printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
-            printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
-            printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
-            printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
-            done
+        do
+        printf "${projectName}_sample${i}" >> "${workDir}/${projectName}.csv"  ##Dummy external sample ID
+        printf ",DummyBarcode${i}" >> "${workDir}/${projectName}.csv" ## Dummy barcode
+        printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
+        printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
+        printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
+        printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
+        printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
+        printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
+        printf "," >> "${workDir}/${projectName}.csv"  ## Gender
+        printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
+        printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
+        printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
+        printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
+        printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
+        printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
         done
+    done
         
 else    
     for ((l=1;l<="${lane}";l++))
-        do
+    do
         while read line
-            do
-            barcode=$(echo "${line}" | cut -d , -f1)
-            externaSampleID=$(echo "${line}" | cut -d , -f2)
-            printf "${externaSampleID}" >> "${workDir}/${projectName}.csv"  ##external sample ID
-            printf ",${barcode}" >> "${workDir}/${projectName}.csv" ## barcode
-            printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
-            printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
-            printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
-            printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
-            printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
-            printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
-            printf "," >> "${workDir}/${projectName}.csv"  ## Gender
-            printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
-            printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
-            printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
-            printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
-            printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
-            printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
-            done < "${informationFile}"
-        done
+        do
+        barcode=$(echo "${line}" | cut -d , -f1)
+        externalSampleID=$(echo "${line}" | cut -d , -f2)
+        printf "${externalSampleID}" >> "${workDir}/${projectName}.csv"  ##external sample ID
+        printf ",${barcode}" >> "${workDir}/${projectName}.csv" ## barcode
+        printf ",${projectName}" >> "${workDir}/${projectName}.csv" ## project
+        printf ",${capturingKit}" >> "${workDir}/${projectName}.csv" ## capturingKit
+        printf ",${sampleType}" >> "${workDir}/${projectName}.csv" ## sampleType
+        printf ",${seqType}" >> "${workDir}/${projectName}.csv" ## seqType
+        printf ",${prepKit}" >> "${workDir}/${projectName}.csv" ## prepKit
+        printf ",${species}" >> "${workDir}/${projectName}.csv" ## species
+        printf "," >> "${workDir}/${projectName}.csv"  ## Gender
+        printf "," >> "${workDir}/${projectName}.csv" ## arrayFile
+        printf ",${l}" >> "${workDir}/${projectName}.csv" ##lane
+        printf ",${sequencingStartDate}" >> "${workDir}/${projectName}.csv" ##sequencingstartdate
+        printf ",${sequencer}" >> "${workDir}/${projectName}.csv" ##sequencer
+        printf ",${run}" >> "${workDir}/${projectName}.csv" ##run
+        printf ",${flowcell}\n" >> "${workDir}/${projectName}.csv" ## flowcell
+        done < "${informationFile}"
+    done
 fi