refactor: consolidate container definitions in one config file

charlie

@@ -220,7 +220,8 @@ sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
     -e "s/HOST/${HOST}/g" \
     -e "s/ADDITIVES/${ADDITIVES}/g" \
     -e "s/VIRUSES/${VIRUSES}/g" \
-    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml > $CONFIGFILE
+    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
+    cat - ${PIPELINE_HOME}/config/containers.yaml > $CONFIGFILE
 fi
 if [ ! -f $WORKDIR/nclscan.config ];then
 sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/resources/NCLscan.config.template > $WORKDIR/nclscan.config
@@ -293,7 +294,9 @@ function reconfig(){
   # rebuild config file and replace the config.yaml in the WORKDIR
   # this is only for dev purposes when new key-value pairs are being added to the config file
   check_essential_files
-  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" ${PIPELINE_HOME}/config/config.yaml > $WORKDIR/config.yaml
+  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
+  ${PIPELINE_HOME}/config/config.yaml |\
+  cat - ${PIPELINE_HOME}/config/containers.yaml > $WORKDIR/config.yaml
   echo "$WORKDIR/config.yaml has been updated!"
 }
 

config/biowulf/config.yaml

@@ -112,20 +112,3 @@ fastas_gtfs_dir: "/data/CCBR_Pipeliner/db/PipeDB/charlie/fastas_gtfs"
 annotation_lookups:
   hg38: "PIPELINE_HOME/resources/hg38_2_hg19_lookup.txt"
   mm39: "PIPELINE_HOME/resources/mm39_circBase_annotation_lookup.txt"
-
-containers:
-  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
-  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
-  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
-  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1"
-  ciri: "docker://nciccbr/charlie_ciri2:v1"
-  clear: "docker://nciccbr/ccbr_clear:2"
-  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1"
-  dcc: "docker://nciccbr/charlie_dcc:v0.2.1"
-  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
-  mapsplice: "docker://cgrlab/mapsplice2:latest"
-  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
-  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
-  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
-  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
-  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.1"

config/containers.yaml

@@ -0,0 +1,16 @@
+containers:
+  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
+  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.1"
+  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
+  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1.0.1"
+  ciri: "docker://nciccbr/charlie_ciri2:v1.0.1"
+  clear: "docker://nciccbr/ccbr_clear:v2.0.1"
+  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1.0.1"
+  dcc: "docker://nciccbr/charlie_dcc:v0.2.1"
+  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
+  mapsplice: "docker://cgrlab/mapsplice2:latest"
+  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
+  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
+  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
+  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
+  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.1"

config/fnlcr/config.yaml

@@ -112,20 +112,3 @@ fastas_gtfs_dir: "/mnt/projects/CCBR-Pipelines/db/charlie/fastas_gtfs"
 annotation_lookups:
   hg38: "PIPELINE_HOME/resources/hg38_2_hg19_lookup.txt"
   mm39: "PIPELINE_HOME/resources/mm39_circBase_annotation_lookup.txt"
-
-containers:
-  base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
-  bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
-  circexplorer: "docker://nciccbr/ccbr_circexplorer:v1.0"
-  circRNA_finder: "docker://nciccbr/charlie_circrna_finder:v1"
-  ciri: "docker://nciccbr/charlie_ciri2:v1"
-  clear: "docker://nciccbr/ccbr_clear:2"
-  cutadapt: "docker://nciccbr/charlie_cutadapt_fqfilter:v1"
-  dcc: "docker://nciccbr/charlie_dcc:v0.2.1"
-  fastqc: "docker://nciccbr/ccrgb_qctools:v4.0"
-  mapsplice: "docker://cgrlab/mapsplice2:latest"
-  multiqc: "docker://nciccbr/ccbr_multiqc_1.15:v1"
-  picard: "docker://nciccbr/ccbr_picard_2.27.5:v1"
-  R: "docker://nciccbr/ccbr_r_4.3.0:v1"
-  star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
-  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.4.1"

docker/bowtie1/meta.yml

@@ -1,4 +1,4 @@
 dockerhub_namespace: nciccbr
 image_name: charlie_bowtie1
-version: v0.1.0
+version: v0.1.1
 container: "$(dockerhub_namespace)/$(image_name):$(version)"