Update scripts default location to follow Maven convention

210c6b69 · bow · c6b4115d · 210c6b69 · 210c6b69 · 210c6b69
Commit 210c6b69 authored Jul 28, 2014 by bow
--- a/bam-metrics/pom.xml
+++ b/bam-metrics/pom.xml
@@ -61,7 +61,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/bam-metrics/scripts/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
+++ b/bam-metrics/scripts/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
--- a/flexiprep/pom.xml
+++ b/flexiprep/pom.xml
@@ -56,7 +56,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/fastqc_contam.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/fastqc_contam.py
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/pyfastqc/__init__.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/pyfastqc/__init__.py
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/qual_type_sickle.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/qual_type_sickle.py
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/seq_stat.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/seq_stat.py
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/sync_paired_end_reads.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/sync_paired_end_reads.py
--- a/gatk/gatk-benchmark-genotyping/pom.xml
+++ b/gatk/gatk-benchmark-genotyping/pom.xml
@@ -61,7 +61,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/gatk/gatk-genotyping/pom.xml
+++ b/gatk/gatk-genotyping/pom.xml
@@ -56,7 +56,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/gatk/gatk-old/pom.xml
+++ b/gatk/gatk-old/pom.xml
@@ -66,7 +66,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/gatk/gatk-pipeline/pom.xml
+++ b/gatk/gatk-pipeline/pom.xml
@@ -76,7 +76,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/gatk/gatk-variantcalling/pom.xml
+++ b/gatk/gatk-variantcalling/pom.xml
@@ -56,7 +56,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/mapping/pom.xml
+++ b/mapping/pom.xml
@@ -66,7 +66,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>

--- a/pipeline-template/pom.xml
+++ b/pipeline-template/pom.xml
@@ -56,7 +56,7 @@
    <build>
        <resources>
            <resource>
-                 <directory>scripts</directory>
+                 <directory>src/main/scripts</directory>
                 <includes>
                     <include>**/*</include>
                 </includes>