Updated Docker

Author: mobinasri

Makefile

@@ -1,7 +1,7 @@
 # Definitions
 repository = mobinasri
 identifier = secphase
-version = v0.4.1
+version = v0.4.2
 git_commit ?= $(shell git log --pretty=oneline -n 1 | cut -f1 -d " ")
 name = ${repository}/${identifier}
 tag = ${version}--${git_commit}

README.md

@@ -62,7 +62,7 @@ Two heuristics are applied for increasing specificity:
 
 ### Running Secphase in marker mode
 
-To run Secphase it is recommended to use the docker image `mobinasri/secphase:v0.4.1`.
+To run Secphase it is recommended to use the docker image `mobinasri/secphase:v0.4.2`.
 
 Here are the parameters `secphase` can accept:
 ```
@@ -108,15 +108,15 @@ samtools sort -n -@8 ${INPUT_DIR}/${BAM_PREFIX}.bam > ${INPUT_DIR}/${BAM_PREFIX}
 ## Create secphase index
 docker run \
 	-v ${INPUT_DIR}:${INPUT_DIR} \
-	mobinasri/secphase:v0.4.1 \
+	mobinasri/secphase:v0.4.2 \
 	secphase_index \
 	-i ${INPUT_DIR}/${BAM_PREFIX}.sorted.bam
 
 ## Run Secphase for HiFi alignments
 docker run \
 	-v ${INPUT_DIR}:${INPUT_DIR} \
 	-v ${OUTPUT_DIR}:${OUTPUT_DIR}
-	mobinasri/secphase:v0.4.1 \
+	mobinasri/secphase:v0.4.2 \
 	secphase --hifi \
 	-i ${INPUT_DIR}/${BAM_PREFIX}.sorted.bam \
 	-f ${INPUT_DIR}/${FASTA_PREFIX}.fa \
@@ -128,7 +128,7 @@ docker run \
 docker run \
 	-v ${INPUT_DIR}:${INPUT_DIR} \
 	-v ${OUTPUT_DIR}:${OUTPUT_DIR}
-	mobinasri/secphase:v0.4.1 \
+	mobinasri/secphase:v0.4.2 \
 	secphase --ont \
 	-i ${INPUT_DIR}/${BAM_PREFIX}.sorted.bam \
 	-f ${INPUT_DIR}/${FASTA_PREFIX}.fa \
@@ -162,7 +162,7 @@ For producing a phased vcf file one approach can be aligning all HiFi reads to e
 docker run \
 	-v ${INPUT_DIR}:${INPUT_DIR} \
 	-v ${OUTPUT_DIR}:${OUTPUT_DIR}
-	mobinasri/secphase:v0.4.1 \
+	mobinasri/secphase:v0.4.2 \
 	secphase --ont \
 	-i ${INPUT_DIR}/${BAM_PREFIX}.sorted.bam \
 	-f ${INPUT_DIR}/${FASTA_PREFIX}.fa \
@@ -175,7 +175,7 @@ docker run \
 ### Correcting bam file with secphase output
 
 To swap the pri/sec tags of the reads reported in `*.out.log` and produce a modified bam file you can run the program  `correct_bam`.
-Again it is recommended to run it using the docker image `mobinasri/secphase:v0.4.1`.
+Again it is recommended to run it using the docker image `mobinasri/secphase:v0.4.2`.
 
 Here are the parameters `correct_bam` can accept:
 ```
@@ -214,7 +214,7 @@ To produce the modified bam file: (Here the input bam file can be sorted by refe
 docker run \
 	-v ${INPUT_DIR}:${INPUT_DIR} \
 	-v ${OUTPUT_DIR}:${OUTPUT_DIR} \
-	mobinasri/secphase:v0.4.1 \
+	mobinasri/secphase:v0.4.2 \
 	correct_bam \
 	-i ${INPUT_DIR}/${BAM_PREFIX}.bam \
 	-P ${OUTPUT_DIR}/${SAMPLE_NAME}.out.log \

wdls/workflows/correct_bam.wdl

@@ -22,7 +22,7 @@ task correctBam {
         Int memSize=8
         Int threadCount=8
         Int diskSize=512
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
     }
     command <<<

wdls/workflows/get_secphased_read_ids.wdl

@@ -16,7 +16,7 @@ task getPhasedReadIds{
         Int memSize=16
         Int threadCount=4
         Int diskSize=256
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
     }
     command <<<

wdls/workflows/secphase.wdl

@@ -7,8 +7,8 @@ workflow runSecPhase {
         File? phasedVcf
         File? variantBed
         String secphaseOptions = "--hifi"
-        String secphaseDockerImage = "mobinasri/secphase:v0.4.1"
-        String version = "v0.4.1"
+        String secphaseDockerImage = "mobinasri/secphase:v0.4.2"
+        String version = "v0.4.2"
     }
     call sortByNameAndIndex {
         input:
@@ -49,7 +49,7 @@ task sortByNameAndIndex {
         Int memSize=16
         Int threadCount=8
         Int diskSize=1024
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -100,7 +100,7 @@ task secphaseIndex {
         Int memSize=8
         Int threadCount=4
         Int diskSize=128
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -150,7 +150,7 @@ task secphase {
         Int memSize=32
         Int threadCount=32
         Int diskSize=128
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -213,7 +213,7 @@ task concatLogs {
         Int memSize=2
         Int threadCount=1
         Int diskSize=32
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -253,7 +253,7 @@ task mergeBeds {
         Int memSize=2
         Int threadCount=1
         Int diskSize=32
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -293,7 +293,7 @@ task splitByName {
         Int memSize=16
         Int threadCount=8
         Int diskSize=512
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -336,7 +336,7 @@ task sortByName {
         Int memSize=16
         Int threadCount=8
         Int diskSize=1024
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }
@@ -385,7 +385,7 @@ task sortByContig {
         Int memSize=8
         Int threadCount=4
         Int diskSize=128
-        String dockerImage="mobinasri/secphase:v0.4.1"
+        String dockerImage="mobinasri/secphase:v0.4.2"
         Int preemptible=2
         String zones="us-west2-a"
     }