use $baseDir consistently

loc_sanger.config

@@ -1,21 +1,21 @@
 env {
-    PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH"
-    RATT_HOME = "${ROOTDIR}/RATT"
-    RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
+    PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH"
+    RATT_HOME = "${baseDir}/RATT"
+    RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
     GT_RETAINIDS = "yes"
     PFAM = "/lustre/scratch108/parasites/ss34/pfam/Pfam-A.hmm"
-    SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm"
-    AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus"
-    FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua"
-    PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt"
+    SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm"
+    AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus"
+    FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua"
+    PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt"
 }
 
 params.GO_OBO = "${HOME}/go.obo"
-params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm"
-params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.conf"
-params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.conf"
-params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua"
-params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg"
+params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm"
+params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.conf"
+params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.conf"
+params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua"
+params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg"
 
 executor {
     name = 'local'

loc_sanger_farm.config

@@ -1,21 +1,21 @@
 env {
-    PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH"
-    RATT_HOME = "${ROOTDIR}/RATT"
-    RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
+    PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH"
+    RATT_HOME = "${baseDir}/RATT"
+    RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
     GT_RETAINIDS = "yes"
     PFAM = "/lustre/scratch108/parasites/ss34/pfam/Pfam-A.hmm"
-    SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm"
-    AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus"
-    FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua"
-    PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt"
+    SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm"
+    AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus"
+    FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua"
+    PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt"
 }
 
 params.GO_OBO = "${HOME}/go.obo"
-params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm"
-params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.conf"
-params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.conf"
-params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua"
-params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg"
+params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm"
+params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.conf"
+params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.conf"
+params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua"
+params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg"
 
 process.memory = "2 GB"
 process.clusterOptions = " -R 'select[mem>2048] rusage[mem=2048]' "

loc_travis.config

@@ -1,22 +1,22 @@
 env {
-    PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${ROOTDIR}/ORTHOMCLV1.4:${ROOTDIR}/genometools/bin:${ROOTDIR}/aragorn:${ROOTDIR}/augustus/bin:$PATH"
-    PERL5LIB = "${ROOTDIR}/ORTHOMCLV1.4/:${ROOTDIR}/RATT/:${ROOTDIR}/ABACAS2/:${PERL5LIB}"
-    RATT_HOME = "${ROOTDIR}/RATT"
-    RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
+    PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${baseDir}/ORTHOMCLV1.4:${baseDir}/genometools/bin:${baseDir}/aragorn:${baseDir}/augustus/bin:$PATH"
+    PERL5LIB = "${baseDir}/ORTHOMCLV1.4/:${baseDir}/RATT/:${baseDir}/ABACAS2/:${PERL5LIB}"
+    RATT_HOME = "${baseDir}/RATT"
+    RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite"
     GT_RETAINIDS = "yes"
-    PFAM = "${ROOTDIR}/Pfam-A.hmm"
-    SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm"
-    AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus"
-    FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua"
-    PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt"
+    PFAM = "${baseDir}/Pfam-A.hmm"
+    SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm"
+    AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus"
+    FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua"
+    PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt"
 }
 
-params.GO_OBO = "${ROOTDIR}/go.obo"
-params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm"
-params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.debian.conf"
-params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.debian.conf"
-params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua"
-params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg"
+params.GO_OBO = "${baseDir}/go.obo"
+params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm"
+params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.debian.conf"
+params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.debian.conf"
+params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua"
+params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg"
 
 executor {
     name = 'local'

nextflow.config

@@ -53,14 +53,11 @@ params {
     // output GAF metadata
     TAXON_ID = 4711
     DB_ID = "GeneDB"
-
 }
 
 profiles {
-
 	docker { includeConfig 'loc_docker.config' }
 	sanger { includeConfig 'loc_sanger.config' }
 	sanger_farm { includeConfig 'loc_sanger_farm.config' }
 	travis { includeConfig 'loc_travis.config' }
-
 }