Merge pull request #52 from RoanKanninga/main

new versions of NGS_Automated (and bundles) + NGS_DNA + ConcordanceCheck

c/ConcordanceCheck/ConcordanceCheck-2.2.1.eb

@@ -0,0 +1,36 @@
+name = 'ConcordanceCheck'
+version = '2.2.1'
+namelower = name.lower()
+homepage = 'https://github.com/molgenis/ConcordanceCheck'
+description = """Various scripts to automate and execute the ConcordanceCheck implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Tarball'
+
+#
+# Example URL: https://github.com/molgenis/ConcordanceCheck/archive/2.2.0.tar.gz
+# 
+source_urls = [('http://github.com/molgenis/%s/archive/' % (name))]
+sources = [('%s.tar.gz' % (version))]
+
+checksums = ['4b51ee0963ab9221383489c96b190ce025ca2687e88b8afd5a64e0b013ca5990']
+
+dependencies = [
+       ('CompareGenotypeCalls', '1.8.1', '-Java-8-LTS'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/ConcordanceCheck.sh',
+        'bin/ParseDarwinSamplesheet.sh',
+        'bin/copyConcordanceCheckData.sh',
+        'bin/notifications.sh',
+        'etc/sharedConfig.cfg',
+        'lib/sharedFunctions.bash',
+    ],
+    'dirs': [
+        'etc/cron.d',
+    ]
+}
+
+moduleclass = 'bio'

g/GATK/GATK-3.7-Java-8-LTS.eb

@@ -0,0 +1,30 @@
+name = 'GATK'
+version = '3.7'
+versionsuffix = '-Java-%(javaver)s-LTS'
+
+homepage = 'http://www.broadinstitute.org/gatk/'
+description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute 
+ to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
+ with a primary focus on variant discovery and genotyping as well as strong emphasis on 
+ data quality assurance. Its robust architecture, powerful processing engine and 
+ high-performance computing features make it capable of taking on projects of any size."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+easyblock = 'Tarball'
+
+# download manually from http://www.broadinstitute.org/gatk/download
+sources = ['GenomeAnalysisTK-%(version)s.tar.bz2']
+checksums = ['11c4d69a2fbb0043a88cf5b9a35fac97']
+
+dependencies = [
+    ('Java', '8', '-LTS'),
+]
+
+modloadmsg = """To execute GATK run: java -jar \\${EBROOTGATK}/GenomeAnalysisTK.jar"""
+
+sanity_check_paths = {
+    'files': ["GenomeAnalysisTK.jar"],
+    'dirs': ["resources"],
+}
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.1.0-GAP-2.7.0.eb

@@ -0,0 +1,19 @@
+name = 'NGS_Automated'
+version = '4.1.0'
+namelower = name.lower()
+versionsuffix = "-GAP-2.7.0"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('GAP', '2.7.0'),
+    ('NGS_Automated', '4.1.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'
+

n/NGS_Automated/NGS_Automated-4.1.0-NGS_DNA-4.2.2.eb

@@ -0,0 +1,18 @@
+name = 'NGS_Automated'
+version = '4.1.0'
+namelower = name.lower()
+versionsuffix = "-NGS_DNA-4.2.2"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('NGS_DNA', '4.2.2','',('foss','2022a')),
+    ('NGS_Automated', '4.1.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.1.0-NGS_Demultiplexing-2.5.3.eb

@@ -0,0 +1,17 @@
+name = 'NGS_Automated'
+version = '4.1.0'
+namelower = name.lower()
+versionsuffix = "-NGS_Demultiplexing-2.5.3"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('NGS_Automated', '4.1.0','-bare'),
+    ('NGS_Demultiplexing', '2.5.3'),
+]
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.1.0-bare.eb

@@ -0,0 +1,30 @@
+name = 'NGS_Automated'
+version = '4.1.0'
+namelower = name.lower()
+versionsuffix='-bare'
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Tarball'
+
+#
+# Example URL: https://github.com/molgenis/NGS_Automated/archive/1.0.1.tar.gz
+# 
+source_urls = [('http://github.com/molgenis/%s/archive/' % (name))]
+sources = [('%s.tar.gz' % (version))]
+
+checksums = ['8b82c8cf423cd1bc6621c0e2ea8b34485c3001fbe986bd1690f9c96b0e8aff62']
+
+sanity_check_paths = {
+    'files': [
+        'bin/cleanupDataOnTmp.sh',
+        'etc/umcg-pr.cfg',
+    ],
+    'dirs': [
+        'bin/',
+        'lib',
+    ]
+}
+
+moduleclass = 'bio'

n/NGS_DNA/NGS_DNA-4.2.2-foss-2022a.eb

@@ -0,0 +1,60 @@
+easyblock = 'Tarball'
+
+name = 'NGS_DNA'
+version = '4.2.2'
+namelower = name.lower()
+
+homepage = 'https://github.com/molgenis/NGS_DNA'
+description = """NGS_DNA pipeline used in the UMCG"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+javaver = '8-LTS'
+py3ver = '3.10.4'
+py2ver = '2.7.16'
+
+#
+# Example URL: https://github.com/molgenis/NGS_DNA/archive/3.2.3.tar.gz
+#
+source_urls = [('http://github.com/molgenis/%s/archive/' % (name))]
+sources = [('%s.tar.gz' % (version))]
+checksums = ['239575a0b2ae1a1f4d620625906b8209eac6db62c37a5b2ff74b46bb01a5317f']
+
+#
+# Dependencies.
+#
+dependencies = [
+#    ('VCFped','20180527_d1bbdf5','-Python-%s' % (py2ver),('foss','2018b')),
+#    ('manta','1.6.0'),
+#    ('CADD', 'v1.4','',('foss','2018b')),
+    ('BCFtools', '1.16'),
+    ('BEDTools', '2.30.0'),
+    ('BWA', '0.7.17-20220923-139f68f'),
+    ('FastQC', '0.11.9', '-Java-%s' % (javaver), ('system', '')),
+    ('GATK', '4.2.4.1', '-Java-8-LTS', ('system', '')),
+    ('gVCF2BED','1.0.0'),
+    ('jq','1.6'),
+    ('HTSlib', '1.16'),
+    ('ngs-utils', '22.10.1','',('system','')),
+    ('pigz', '2.7',''),
+    ('picard', '2.26.10', '-Java-%s' % (javaver), ('system', '')),
+    ('gavin-plus', '1.5.0', '-Java-%s' % (javaver), ('system', '')),
+    ('io_lib', '1.14.11'),
+    ('Molgenis-Compute', '20.03.1', '-Java-11-LTS', ('system', '')),
+    ('multiqc', '1.12'),
+    ('R','4.2.1','-bare'),
+    ('sambamba', '0.7.0', '', ('system', '')),
+    ('SAMtools', '1.16.1'),
+    ('seqtk', '1.3'),
+    ('snpEff', '4.3t', '-Java-%s' % (javaver), ('system', '')),
+    ('vcfanno', 'v0.3.3', '', ('system', '')),
+]
+
+
+sanity_check_paths = {
+    'files': ['workflow_DRAGEN.csv', 'parameters.csv'],
+    'dirs': []
+}
+
+moduleclass = 'bio'
+modextrapaths = {'PATH': ['scripts/']}