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Merge pull request #9 from mobinasri/dev-v0.4.1
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fixed a bug in the marker mode
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@mobinasri
mobinasri committed Jul 6, 2023
2 parents 8fcefb1 + c61359e commit 70d82cc
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Showing 5 changed files with 20 additions and 20 deletions.
2 changes: 1 addition & 1 deletion Makefile
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@@ -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}
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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -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:
```
Expand Down Expand Up @@ -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 \
Expand All @@ -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 \
Expand Down Expand Up @@ -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 \
Expand All @@ -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:
```
Expand Down Expand Up @@ -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 \
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2 changes: 1 addition & 1 deletion wdls/workflows/correct_bam.wdl
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Expand Up @@ -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 <<<
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2 changes: 1 addition & 1 deletion wdls/workflows/get_secphased_read_ids.wdl
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Expand Up @@ -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 <<<
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20 changes: 10 additions & 10 deletions wdls/workflows/secphase.wdl
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Expand Up @@ -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:
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
Expand Down Expand Up @@ -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"
}
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